microsoft...brian shoichet, cv august, 2016 university of california brian shoichet, curriculum...

Brian Shoichet, CV August, 2016

University of California Brian Shoichet, Curriculum Vitae

Name: Brian Shoichet, Ph.D. Position Professor, Step VII, Dept. of Pharmaceutical Chemistry

Address University of California, San Francisco

1700 4th St., Byers Hall Rm 508D San Francisco, CA 94158-2550

e-mail: [email protected]

Citizenship Canada, Born: 06/27/63 US Permanent Resident Education 1981-1985 Massachusetts Institute of Technology B.Sc. in Chemistry; B.Sc. in History

1986-1991 University of California, San Francisco Ph.D. in Pharmaceutical Chemistry, Advisor Professor Irwin Kuntz

Postdoctoral Research 1992 University of California, San Francisco, Professor Irwin Kuntz 1993-1996 Institute of Molecular Biology, Eugene, Oregon, Professor Brian Matthews Principal Positions Held: 1996-2002 Assistant Professor of Molecular Pharmacology & Biological Chemistry 2002-2003 Associate Professor (tenured), Mol. Pharmacology & Biological Chemistry Northwestern University

2003-2005 Associate Professor of Pharmaceutical Chemistry 2005-2013 Professor (Step VII) of Pharmaceutical Chemistry 2011-2012 Vice Chair, Dept. of Pharmaceutical Chemistry, UCSF 2012-2013 Director, California Institute for Quantitative Biology of UCSF (QB3) 2013-2014 Adjunct Professor of Pharmaceutical Chemistry (WOS) University of California, San Francisco

2013-2014 Professor, Faculty of Pharmacy 2014-Present Adjunct Professor, Faculty of Pharmacy (Courtesy Appt) University of Toronto

2014-Present Professor of Pharmaceutical Chemistry, Step VII University of California, San Francisco

Keywords: Molecular recognition, drug discovery, structure-based inhibitor discovery, computational chemical biology, systems pharmacology, molecular docking, promiscuous inhibition, G-Protein Coupled Receptors.

Honors & Awards 1993-1996 Damon Runyon-Walter Winchell Cancer Research Fellow 1997-1999 PhRMA Foundation Career Development Award 1998-2003 National Science Foundation CAREER Award 2001 Dean’s Award for Teaching Excellence (Northwestern University) 2004 Astra Lectureship, University of Ottawa 2006-2007 Novartis Chemistry Lecturer (Cambridge, Basel, Vienna, Horsham, Tsukuba, Emeryville) 2008 Swiss Universities 3e Cycle en Chimie (Lausanne, Bern, Friborg, Geneva) 2009 Abbott Lectureship, Yale University 2011 Society for Biomolecular Sciences Accomplishment Award

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2011 Topliss Lectureship, University of Michigan 2013 Distinguished Scientist Seminar, University of Pittsburgh 2014 Distinguished Scientist Lectureship, University of Ohio School of Pharmacy 2014 Center for Mol. Innovation in Drug Discovery, Northwestern University, Annual Keynote 2015 Cambridge Healthtech 10th Annual Drug Discovery Chemistry, Plenary Keynote. 2015 Arthur Broom Lecture, University of Utah School of Pharmacy. 2015 International Chair of Therapeutic Innovation, CNRS, Paris. 2016 Molecular Graphics & Modeling Society, Erlangen, Germany. Plenary Keynote. 2016 Partnership for Excellence in Structural Biology Annual Symposium, UConn. Keynote 2017 Delano Award, ASBMB

Professional & Scientific Activity Editorial Service 1993-present Ad hoc reviewer for J. Mol. Biol., Proc. Natl. Acad. Sci., Chemistry & Biology,

Protein Sci., Proteins, J. Am. Chem. Soc., J. Med. Chem., J. Chem. Inf. Modeling, Protein Eng., J.Biol. Chem., Nature Biotech., Nature Struct. Biol., Nature Chemical Biology, Nature Chemistry, Nature, and Science.

1999-2000 Editorial Board of Journal Of Computer-Aided Molecular Design 1999-2003 Editorial advisory board of PharmSci, Amer. Assoc. of Pharmaceutical Sciences 2001-2003 Faculty of 1000 (Ligand-Macromolecular Interactions & Inhibitor Design) 2001-2003 Editor-in-Chief of Journal Of Computer-Aided Molecular Design 2005-present International Advisory Board Molecular Biosciences, Royal Soc. Chem. 2005-2010 Editorial Advisory Board Journal of Medicinal Chemistry 2016-2017 Editorial Advisory Board, Journal of Chemical Information & Modeling 2016-2017 Editorial Advisory Board, ACS Chemical Biology Conferences & Sessions Organized 1998 Midwest Enzyme Chemistry Conference, Northwestern University. 2001 Computational Structural Biology (Session on Docking), FSU, Tallahasse FL 2001 Docking & Testing Session, ACS National Meeting, Chicago IL 2002 Structure-based drug design, Cambridge HealthTech Institute, Boston MA 2003 Structure-based drug design, Cambridge HealthTech Institute, Boston MA 2005 NIH Meeting on Docking & Scoring, Washington DC (co-chair) 2006 Structure-Based Drug Design Keystone Conference, Whistler BC (co-chair) 2007 Gordon Research Conference in Computer-Aided Drug Discovery, New Hampshire

(vice chair) 2009 ASBMB National Meeting, New Orleans LA (co-chair), April 18-22 2009 Gordon Research Conference in Computer-Aided Drug Discovery, New Hampshire

(chair). July 19-24 2009 Nature Chem. Biol. Drug Discovery Meeting, Boston MA (co-chair) 2010 Gordon Research Conference in Biomolecular Interactions and Methods, session

chair in drug discovery (January, Galveston Tx) 2015-2016 Scientific Advisory Board of the 21st EuroQSAR Symposium Scientific Advisory Boards, Consulting & Companies Founded 1998-2003 SAB Synergix, Cue Biotech, Ctr for Molecular Design (Univ of Toronto) 2001-2003 Consultant for Pharmacia Corp.; Procter & Gamble Pharmaceuticals 2001-2004 Consultant for Protein Pathways, Cytoclonal Pharma, Syrrx, Epix Medical 2002-2008 Consultant for Structural GenomiX 2004-2008 SAB, NIH RoadMap Chemical Libraries and Screening Initiative 2005 Consultant for Scios; Consultant for Novartis 2005-2006 Consultant for Boehringer Ingelheim

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2006-2007 Consultant for CropSolutions Inc. 2006-2008 SAB for Buck Institute. 2007-2009 Consultant for Eli Lilly & Co. 2008-2009 SAB for Chicago Tri-Institutional Center for Chemical Methods and Library

Development 2009-2012 Scientific Advisory Group for Corning Life Sciences 2009-2011 Worldwide consultant for Pfizer Comp. Chem. 2012 Consultant for Alios Pharma 2009-2011 Consultant for Anacor Pharma 2008-2012 Consultant for Vitae Pharmaceuticals 2009-2015 Consultant for ZoBio Pharma 2014 Consultant for AstraZeneca 2015 External Advisory Board, University of Pittsburgh Drug Discovery Institute

2009 Founder, SeaChange Pharmaceuticals 2016 Founder, Epiodyne Pharmaceuticals

Research Program An overarching goal of our lab is bringing chemical reagents to biology, using a combination of

computational simulation and experiment. Using a protein-centric approach, we search for new ligands that complement protein structures. This typically involves molecular docking and the development of model experimental systems to experimentally test new algorithms that we develop. A new direction adopts a ligand-centric approach that seeks new targets for known drugs. Whereas this lacks the physical foundation of the structure-based docking, it returns to an older, pharmacological view of biological relationships, bringing to it a quantitative model. A biological focus for both areas is the discovery of reagents to modulate GPCRs.

As part of our research, we have introduced free community resources: 1. The ZINC database of commercially available, dockable molecules: http://zinc.docking.org. 2. The DUD benchmark of 40 targets, 3000 ligands & 97000 decoys: http://dud.docking.org. 3. DOCK Blaster, a web-based community tool for docking: http://blaster.docking.org. 4. SEA, a chemoinformatics method for predicting targets for ligands: http://sea.docking.org. 5. Procedures and reagents for counterscreening for promiscuous aggregation. 6. Libraries of ligands and decoys for model binding sites for testing docking:

http://shoichetlab.compbio.ucsf.edu/take-away.php.

Six recent papers representative of the interests of my laboratory: E Lounkine†, et al., BK Shoichet* & L Urban* Large Scale Prediction and Testing of Drug Activity

on Side-Effect Targets. Nature 486, 361-7. (2012).

H Lin, MF Sassano, BL Roth* and BK Shoichet*. A Pharmacological Organization of G Protein-coupled Receptors. Nature Methods 10, 140-6 (2013).

M Fischer, RG Coleman, JS Fraser* & BK Shoichet*. Incorportation of protein flexibility & conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry 6, 575-83 (2014).

London N, et al., Shoichet BK* & Taunton J*. Covalent docking of large libraries for the discovery of chemical probes. Nature Chem Biol. 10, 1066-72 (2014).

XP Haung, J. Karpiak, WK Kroeze, et al, BK Shoichet* & BL Roth*. Allosteric ligands for the pharmacologically dark receptors GPR68. Nature 527, 477-83 (2015).

McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK*, Shoichet MS*. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol. (Jan 15, 2016).

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http://zinc.docking.org/

http://dud.docking.org/

http://blaster.docking.org/

http://sea.docking.org/

http://shoichetlab.compbio.ucsf.edu/take-away.php


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Peer Reviewed Publications (168 total, Google Scholar H-index 81) 1. Sowdhamini, R.; Srinivasan, N.; Shoichet, BK.; Santi, DV.; Ramakrishnan, C & Balaram, P*;

Stereochemical Modeling of Disulfide Bridges. Protein Engineer., 3(2): 95-103 (1989).

2. BK Shoichet & ID Kuntz.* Protein docking and complementarity. J. Mol. Biol. 221, 327-346 (1991)

3. Shoichet, BK, Bodian, DL & Kuntz, ID*; Molecular Docking Using Shape Descriptors. J. Comput Chem. 13, 380-397 (1992).

4. Meng, E.C.; Shoichet, B.K. & Kuntz, I.D.*; Automated Docking with Grid-Based Energy Evaluation. Journal of Computational Chemistry 13, 504-524. (1992).

5. Shoichet, B.K.; Stroud, R.M.; Santi, D.V.; Kuntz, I.D* & Perry, K.M.; Structure Based Inhibitor Discovery in Thymidylate Synthase. Science 259, 1445-1449 (1993).

6. BK Shoichet & ID Kuntz.* Matching chemistry and shape in molecular docking, Protein. Engineer, 6, 723-32 (1993).

7. U. Schellenberger, VS Francis, P. Balaram, BK Shoichet, & DV Santi.* Designed deletion of an entire domain of Lactobacillus thymidylate synthase gives a catalytically active enzyme. Biochemistry, 33, 5623-5629 (1994).

8. Shoichet, B.K; Baase, W.A.; Kuroki, R. & Matthews, B.W.*; A Relationship Between Protein Stability and Protein Function. Proc. Nat. Acad. Sci. 92, 452-456 (1995).

9. Zhang, X.J.; Baase, W.A.; Shoichet, B.K.; Wilson, K. & Matthews, B.W.*; Incremental Enhancement of Protein Stability by the Combination of Point Mutations in T4 Lysozyme. Protein Engineer 8, 1017-1022 (1995).

10. Strynadka, NCJ, Eisenstein, M, Katchalski-Katzir, E, Shoichet, BK, et al. & James, MNG*; Molecular Docking Programs Successfully Predict the Binding of a Beta-Lactamase Inhibitory Protein to the TEM-1 Beta-Lactamase. Nat. Struct. Biol. 3, 233-239 (1996).

11. Gassner, N.C., Baase, W.A., Linstrom, J.D., Shoichet, B.K. & Matthews, B.W*. Isolation and Characterization of Multiple Methionine Mutants of T4 Lysozyme with a Simplified Core. Techniques in Protein Chemistry, VII 851-863 (1997).

12. Lorber, D.A. & Shoichet, B.K.*, Flexible Ligand Docking Using Conformational Ensembles. Protein Science, 7, 938-950 (1998).

13. Morosini, M.-I.; Negri, M.-C.; Shoichet, B.; M.-R. Baquero; Baquero, F. and Blazquez, J.*; An extended-spectrum AmpC-type β-lactamase obtained by in vitro antibiotic selection. FEMS Microbiology Letters, 165, 85-90 (1998).

14. Weston, GS.; Blasquez, J; Baquero, F, and Shoichet, BK*; Structure-based Enhancement of Boronic Acid Based Inhibitors of AmpC β-lactamase. J. Med. Chem., 41: 4577-4586 (1998).

15. KC Usher, LC Blaszczak, GS Weston, BK Shoichet* & SJ Remington*; The three dimensional structure of AmpC β-lactamase from Escherichia coli bound to a transition state analog: possible implications for the oxyanion hypothesis and for inhibitor design. Biochemistry 37,16082-16092 (1998).

16. Shoichet, B.K.*; Leach, A. & Kuntz, I.D*; Ligand Solvation Effects in Molecular Docking. Proteins 34, 4-16, (1999).

17. BM Beadle, WA Baase, D. Wilson, NR Gilkes & BK Shoichet* Comparing the Thermodynamic Stabilities of a Thermophilic and a Mesophilic Enzyme. Biochemistry 38, 2570-2576 (1999).

18. Stout, T.J.; Tondi, D., Rinaldi, M., Barlocco, D., Pecorari, P., Santi, D.V., Kuntz, I.D., Stroud*, R.M., Shoichet, B.K.* & Costi, M.P.* Structure-Based Design of Inhibitors Specific for Bacterial Thymidylate Synthase. Biochemistry 38, 1607-1617 (1999).

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19. Tondi, D., Slomczsynska, U., Watterson, D.M., Costi, M.P., Ghelli, S & Shoichet, B.K.*, Structure-Based Discovery and In-Parallel Elaboration of Novel inhibitors of Thymidylate Synthase. Chemistry & Biology 6, 319-331 (1999).

20. Beadle, B.M., McGovern, S.L., Patera, A. & Shoichet, B.K.* Functional Analyses of AmpC β-Lactamase Through Differential Stability. Protein Science 8, 1816-1824 (1999).

21. Powers, R.A., Blazquez, J., Weston G.S., Morosini, M.I., Baquero F. & Shoichet, B.K.* The Complexed Structure and Anti-Microbial Activity of a Non- β-Lactam Inhibitor of AmpC β-lactamase. Protein Science, 8, 2330-2337 (1999).

22. A Patera, LC Blaszczak & BK Shoichet.* Crystal structures of substrate and inhibitor complexes with AmpC β-lactamase: possible implications for substrate-assisted catalysis. J. Am. Chem. Soc. 122, 10504-10512 (2000).

23. E Caselli, RA Powers, LC Blaszczak, CY Wu, F Prati & BK Shoichet.* Energetic, structural & anti-microbial analyses of β-lactam side chain recognition by β-lactamases. Chem.& Biol 8, 10-17 (2001).

24. Su, A.I, Lorber, D.M., Weston, G.S., Baase, W.A, Matthews, B.W. & Shoichet, B.K.* Docking Molecules by Families to Increase the Diversity of Hits in Database Screens: Computational Strategy and Experimental Evaluation. Proteins 42:279–293 (2001).

25. Beadle, BM, Nicholas, RA & Shoichet, BK* Interaction energies between β-lactam antibiotics and a penicillin binding protein by reversible thermal denaturation. Protein Science 10, 1254-9 (2001)

26. D Tondi, RA Powers, MC Negri, E Caselli, J Blazquez, MP Costi* & BK Shoichet* Structure-based design & in-parallel synthesis of inhibitors of AmpC β-lactamase. Chem. & Biol. 8, 593-611 (2001).

27. Trehan, I, Beadle, B.M., & Shoichet, B.K.* Inhibition of AmpC β-Lactamase Through a Destabilizing Interaction in the Active Site. Biochemistry 40, 7992-7999 (2001).

28. Powers, R.A., Caselli, E., Focia, P., Prati, F. & Shoichet, B.K.* The Structures of Ceftazidime and its Transition-State Analog Bound to AmpC β-lactamase: Implications for Inhibition, Mechanism and Resistance. Biochemistry 40, 9207-14 (2001).

29. Wang, X., Minasov, G. & Shoichet, B.K.* Interaction Energies in Covalent Complexes: TEM-1 β-lactamase and β-lactams. Proteins 47, 86-96 (2002).

30. Lorber, D.M., Udo, M.K., & Shoichet, B.K.* Protein-Protein Docking with Multiple Ligand Residue Conformations and Multiple Residue Identities. Protein Science, 11, 1393-1408 (2002).

31. BM Beadle, I Trehan, P Focia & BK Shoichet.* Structural milestones in the pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC β-lactamase. Structure 10, 413-424 (2002).

32. SL McGovern, E Caselli, N Grigorieff & BK Shoichet* A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening. J. Med. Chem. 45, 1712-1722 (2002).

33. G. Minasov, X. Wang. & B.K. Shoichet* An ultra-high resolution structure of TEM-1 β-lactamase suggests a role for Glu166 as the general base in acylation. J. Am. Chem. Soc. 124, 5333-40 (2002)

34. Doman, T.N*, McGovern, S.L., Witherbee, B.J., Kasten, T.P., Kurumbail, R., Stallings, W.C., Connolly, D.T., & Shoichet, B.K.* Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1B. J. Med. Chem. 45, 2213-2221 (2002).

35. Wang, X., Minasov, G., & Shoichet, B.K.* Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-Offs. J. Mol. Biol. 320, 85-95 (2002).

36. Powers, R.A. & Shoichet, B.K.* Mapping the Active Site of AmpC β-Lactamase for Hot-Spots. J. Med. Chem. 35, 3222-3234 (2002).

37. Powers, R.A., Morandi, F. & Shoichet, B.K.* Structure-based discovery of a novel, non-covalent

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inhibitor of AmpC β-lactamase. Structure 10, 1013-1023 (2002)

38. B.M. Beadle and B.K. Shoichet.* Structural bases of stability-function trade-offs in enzymes. J. Mol. Biol. 321, 285-296 (2002)

39. Wang, X. Minasov, G. & Shoichet, B.K.* Inhibitor Resistance Mechanisms Revealed by TEM-30, TEM-32, and TEM-34 structures. J. Biol. Chem. 277, 32149-32156 (2002)

40. Trehan, I., Morandi, F. & Shoichet, B.K.* Using Steric Hindrance to Design New Inhibitors of Class C β-Lactamases. Chemistry & Biology 9, 971-980 (2002).

41. BQ Wei, WA Baase, L Weaver, BW Matthews* & BK Shoichet*. A Model Binding Site for Testing Scoring Functions in Molecular Docking. J. Mol. Biol. 322, 339-355 (2002).

42. B.M. Beadle and B.K. Shoichet.* A structural basis for imipenem inhibition of class C β-lactamases. Antimicrobial Agents in Chemotherapy 46(12), (Dec, 2002).

43. F. Morandi, E. Caselli, S. Morandi, P.J. Focia, J. Blazquez, B.K. Shoichet* and F. Prati*. Nanomolar inhibitors of AmpC β-lactamase. J. Am. Chem. Soc, 125, 685-695 (2003).

44. S.L. McGovern & B.K. Shoichet.* Kinase Inhibitors: not just for kinases anymore. J. Med. Chem. 46, 1478-1483 (2003).

45. CE Atreya, EF Johnson, JJ Irwin, et al. BK Shoichet & Anderson KS*. A molecular docking strategy identifies eosin B as a non-active site inhibitor of protozoal bifunctional thymidylate synthase-dihydrofolate reductase. J Biol Chem. 278, 14092-100 (2003)

46. S. Soelaiman, BQ Wei, et al, BK Shoichet* & W-J Tang*. Structure-based inhibitor discovery against adenylyl cyclase toxins from pathogenic bacteria that cause anthrax and whooping cough. J. Biol. Chem. 278, 25990-7 (2003).

47. S.L. McGovern & B.K. Shoichet.* Information decay in molecular docking screens with decreasing definition of the receptor binding site. J. Med. Chem., 46, 2895-2907 (2003).

48. X. Wang, G. Minasov & B.K. Shoichet.* Recognition and Resistance in TEM β-lactamase. Biochemistry 42, 8434-8444 (2003).

49. SO Meroueh, G Minasov, W Lee, BK Shoichet, S Mobashery.* Structural aspects for evolution of beta-lactamases from penicillin-binding proteins. J Am Chem Soc. 125, 9612-8 (2003)

50. SL McGovern, B. Helfand, B. Feng & BK Shoichet.* A Specific Mechanism for Non-Specific Inhibition. J. Med. Chem. 46, 4265-72 (2003).

51. J. Seidler, SL McGovern, TN Doman & BK Shoichet.* Identification and Prediction of Promiscuous Drugs. J. Med. Chem. 46, 4477-4486 (2003)

52. T. Roth, G. Minasov & BK Shoichet.* Thermodynamic Cycle Analysis & Inhibitor Design Against β-lactamase. Biochemistry 42, 14483-91 (2003).

53. J Horn & BK Shoichet* Allosteric inhibition through core disruption. J. Mol. Biol. 336, 1283-91 (2004)

54. BQ Wei, L Weaver, AM Ferrari, BW Matthews* & BK Shoichet.* Testing a flexible-receptor docking algorithm in a model binding site. J. Mol. Biol. 337, 1161-82 (2004).

55. AM Ferrari, BQ Wei, L. Costantino & BK Shoichet.* Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 47, 5076-84 (2004).

56. JJ Irwin* & BK Shoichet.* ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Comput Sci. 45, 177-82 (2005)

57. Y Chen, J Delmas, J Sirot, BK Shoichet* & R Bonnet.* Atomic resolution structures of CTX-M β-lactamases: extended spectrum activities from increased mobility and decreased stability. J. Mol. Biol 348, 349-62 (2005).

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58. Y Chen, BK Shoichet* & Richard Bonnet.* Structure, function & inhibition along the reaction coordinate of CTX-M β-lactamases. J. Am. Chem. Soc. 127, 5423-34 (2005).

59. D Tondi, F Morandi, R Bonnet, MPCosti & BK Shoichet.* Structure-based optimization of a non-β-lactam lead results in inhibitors that do not up-regulate β-lactamase expression in cell culture. J. Am. Chem. Soc. 127, 4632-9 (2005).

60. AP Graves, R Brenk & BK Shoichet*. Decoys for Docking. J. Med. Chem. 48, 3714-28 (2005).

61. VL Thomas, D Golemi-Kotra, C Kim, SB Vakulenko, S Mobashery & BK Shoichet.* Structural Consequences of the Inhibitor-Resistant Ser130Gly Substitution in TEM β-Lactamase. Biochemistry 44, 9330-9338 (2005).

62. BY Feng, A Shelat, TN Doman, RK Guy, BK Shoichet*. High-throughput assays for promiscuous inhibitors. Nature Chem. Biol. 1, 146 - 148 (2005)

63. R Brenk, JJ Irwin & BK Shoichet*. Here be dragons: docking and screening in an uncharted region of chemical space. J Biomol Screen. 10, 667-74 (2005).

64. JJ Irwin, FM Raushel & BK Shoichet*. Virtual Screening against Metalloenzymes for Inhibitors and Substrates. Biochemistry 44, 12316-28 (2005)

65. DM. Lorber and Brian K. Shoichet* Hierarchical Docking of Databases of Multiple Ligand Conformations. Current Topics Med. Chem. 5, 739-749 (2005).

65. R Brenk, S Vetter, SE Boyce, DB Goodin & BK Shoichet.*. Probing molecular docking in a charged model binding site. J. Mol. Biol. 357, 1449-70 (2006).

66. Y Chen, G Minasov, TA Roth, F Prati & BK Shoichet.* The Deacylation Mechanism of AmpC β-lactamase at Ultra-High Resolution. J. Am. Chem. Soc. 128, 2970-6 (2006).

67. BY Feng & BK Shoichet.* Synergy and Antagonism of Promiscuous Inhibition in Multiple-Compound Mixtures. J. Med. Chem. 49, 2151-4 (2006).

68. BK Shoichet. Interpreting Steep Dose-Response Curves in Early Inhibitor Discovery. J Med Chem. 49, 7274-7277 (2006).

69. K Babaoglu & BK Shoichet.* Deconstructing Fragment-based Inhibitor Discovery. Nat. Chem. Biol 2, 720-3 (2006).

70. Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ*, Shoichet BK.* Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc. 128,15882-91 (2006).

71. Nowlan C, Li Y, Hermann JC, Evans T, Carpenter J, Ghanem E, Shoichet BK, Raushel FM. Resolution of Chiral Phosphate, Phosphonate, and Phosphinate Esters by an Enantioselective Enzyme Library. J Am Chem Soc. 128,15892-902 (2006).

72. Niu Huang, Brian K. Shoichet* & John J. Irwin.* Benchmarking Sets for Molecular Docking. J. Med. Chem. 49, 6789-801(2006).

73. KE Coan & BK Shoichet*. Stability and equilibria of promiscuous aggregates in high protein milieus. Mol Biosyst. 3, 208-13 (2007).

74. MJ Keiser, BL Roth, BN Armbruster, P Ernsberger, JJ Irwin, BK Shoichet*. Relating protein pharmacology by ligand chemistry. Nat Biotech 25 (2), 197-206 (2007).

75. BY Feng, A Simeonov, A Jadhav, K Babaoglu, J Inglese, BK Shoichet* & CP. Austin.* A High-throughput Screen for Aggregation-based Inhibition in a Large Compound Library. J. Med. Chem. 50, 2385-90 (2007)

76. Chen Y, Bonnet R, Shoichet BK*. The Acylation Mechanism of CTX-M beta-Lactamase at 0.88 A Resolution. J Am Chem Soc 129, 5378-5380 (2007).

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77. JC Hermann, R Martί-Arbona, AA Fedorov, E Federov, SC Almo, BK Shoichet*, FM Raushel. Structure-based activity prediction for an enzyme of unknown function. Nature (2007).

78. DL Mobley, AP Graves, JD Chodera, AC McReynolds, BK Shoichet*, KA Dill.* Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 371, 1118-34 (2007).

79. A Venturelli, D Tondi1,2, L Cancian, F Morandi G. Cannazza, B Segatore, B Prati, G Amicosante, BK Shoichet & MP Costi*. Optimizing Cell Permeation of an Antibiotic Resistance Inhibitor for Improved Efficacy. J. Med. Chem. 15, 5644-54 (2007).

80. S Morandi, F Morandi, BK Shoichet, E Caselli & F Prati*. Structure-based optimization of cephalothin-analog boronic acids as β-lactamase inhibitors. Bioorg. Med. Chem. Let. in press (2007).

81. Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for Function Trade-Offs in the Enolase Superfamily 'Catalytic Module'. Biochemistry 46, 6688-95 (2007).

82. Wyrembak PN, Babaoglu K, Pelto RB, Shoichet BK, Pratt RF. O-Aryloxycarbonyl Hydroxamates: New β-Lactamase Inhibitors That Cross-Link the Active Site. J Am Chem Soc 129, 9548-9 (2007).

83. BY Feng, BH Toyama, H Wille, DW Colby, SR Collins, BC May, SB Prusiner, J Weissman & BK Shoichet* Promiscuous Small-molecule Aggregates Inhibit Amyloid Polymerization. Nature Chem. Biol 4, 197-199 (2008).

84. J Delmas, Y Chen, F Prati, F Robin, BK Shoichet & R Bonnet*. Structure and dynamics of CTX-M enzymes reveal insights into substrate accommodation by extended-spectrum beta-lactamases. J Mol Biol. 375,192-201.

85. S Morandi, F Morandi, E Caselli, BK Shoichet, F Prati*. Structure-based optimization of cephalothin-analogue boronic acids as β-lactamase inhibitors. Bioorg Med Chem 16, 1195-205 (2008)

86. Venturelli A, Tondi D, Cancian L, Morandi F, Cannazza G, Segatore B, Prati F, Amicosante G, Shoichet BK, Costi MP*. Optimizing cell permeation of an antibiotic resistance inhibitor for improved efficacy. J Med Chem. 50, 5644-54 (2008)

87. K Babaoglu, A Simeonov, JJ Irwin, ME Nelson, B Feng, CJ Thomas, L Cancian, MP Costi, DA Maltby, A Jadhav, J Inglese, CP Austin* & BK Shoichet*. A Comprehensive mechanistic analysis of hits from high-throughput and docking screens against β-Lactamase. J Med Chem 51, 2502-08 (2008)

88. J. Hert, MJ Keiser, JJ Irwin, TI Oprea & BK Shoichet.* Quantifying the relationships among drug classes. J. Chem. Inf. Model. 48, 755-65 (2008).

89. AP Graves, DM Shivakumar, SE Boyce, MP Jacobson, DA Case, & BK Shoichet.* Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J. Mol. Biol. 377, 914-34 (2008).

90. KE Coan & BK Shoichet. Stoichiometry and physical chemistry of promiscuous aggregate-based inhibitors. J Am Chem Soc 130, 9606-12 (2008).

91. N Huang & BK Shoichet. Exploiting ordered waters in molecular docking. J Med Chem 51, 4862-5.

92. Marciano DC, et al., Shoichet BK, Palzkill T. Genetic and Structural Characterization of an L201P Global Suppressor Substitution in TEM-1 beta-Lactamase. J Mol Biol. Sep 16 e-pub (2008).

93. Y Chen and BK Shoichet* Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nature Chem. Biol. 5, 358-64 (2009).

94. J Hert, JJ Irwin, C Laggner, MJ Keiser & BK Shoichet*. Quantifying Library Bias in Screening Success. Nature Chem. Biol. 5, 479-83 (2009).

95. P Kolb1,*, DM Rosenbaum2,*, JJ Irwin1, JJ Fung, BK Kobilka* & BK Shoichet*. Structure-based discovery of β2-adrenergic receptor ligands. Proc. Natl. Acad. Sci. 106, 6843-8 (2009).

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96. DG Teotico, K Babaoglu, et al & BK Shoichet. Docking for fragment inhibitors of AmpC β-lactamase: hit-rates, structures and chemical space. Proc. Natl. Acad. Sci. 106, 7455-60 (2009). PMC2671983

97. KE Coan, DA Maltby, AL Burlingame & BK Shoichet. Promiscuous Aggregate-Based Inhibitors Promote Enzyme Unfolding. J Med Chem 52, 2067-2075 (2009). PMCID: PMC2664636

98. RS Ferreira, C Bryant, KK Ang, JH McKerrow, BK Shoichet, AR Renslo. Divergent Modes of Enzyme Inhibition in a Homologous Structure-Activity Series. J Med Chem. 2009 Jul 28 E-pub. PMID: 19637873

99. JJ Irwin, BK Shoichet, MM Mysinger, N Huang, F Colizzi, P Wassam, Y Cao. Automated docking screens: a feasibility study. J Med Chem. 52 5712-20 (2009). PMID: 19719084

100. SE Boyce, DL Mobley, GJ Rocklin, AP Graves, KA Dill, BK Shoichet..Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. J Mol Biol. 394, 747-63 (2009). PMC2788029

101. Y. Chen, W Zhang, Q Shi, D Hesek, M Lee, S Mobashery, BK Shoichet. Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc. 131, 14345-54 (2009). PMID: 19807181

102. H Fan, JJ Irwin, BM Webb, G Klebe, BK Shoichet*, Sali A*. Molecular Docking Screens Using Comparative Models of Proteins. J Chem Inf Model. 49, 2512-27 (2009). PMID: 19845314

103. MJ Keiser, V Setola, JJ Irwin et al., BK Shoichet* & BL Roth. Predicting new molecular targets for known drugs. Nature, 462, 175-81 (2009).

104. Hall RS, Fedorov AA, Marti-Arbona R, Fedorov EV, Kolb P, Sauder JM, Burley SK, Shoichet BK, Almo SC, Raushel FM. The hunt for 8-oxoguanine deaminase. J Am Chem Soc. 132, 1762-3 (2010) PMID: 20088583.

105. Mott BT, Ferreira RS, Simeonov A, Jadhav A, Ang KK, Leister W, Shen M, Silveira JT, Doyle PS, Arkin MR, McKerrow JH, Inglese J, Austin CP, Thomas CJ, Shoichet BK, Maloney DJ. Identification and optimization of inhibitors of Trypanosomal cysteine proteases: cruzain, rhodesain, and TbCatB. J Med Chem., 53 52-60. (2010) PMID: 19908842.

106. Jadhav A, Ferreira RS, Klumpp C, Mott BT, Austin CP, Inglese J, Thomas CJ, Maloney DJ, Shoichet BK, Simeonov A. Quantitative analyses of aggregation, autofluorescence, and reactivity artifacts in a screen for inhibitors of a thiol protease. J Med Chem. 53, 37-51 (2010)

107. Cummings JA, Nguyen TT, Fedorov AA, Kolb P, Xu C, Fedorov EV, Shoichet BK, Barondeau DP, Almo SC, Raushel FM. Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase. Biochemistry 49, 611-22. (2010) PMID: 20000809

108. Thomas VL, McReynolds AC, Shoichet BK. Structural bases for stability-function tradeoffs in antibiotic resistance. J Mol Biol. 396, 47-59 (2010) PMID: 19913034

109. Kokel D, Bryan J, Laggner C, White R, Cheung CY, Mateus R, Healey D, Kim S, Werdich AA, Haggarty SJ, Macrae CA, Shoichet B, Peterson RT. Rapid behavior-based identification of neuroactive small molecules in the zebrafish. Nat Chem Biol. 6, 231-237 (2010).PMID: 20081854

110. Degraw AJ, Keiser MJ, Ochocki JD, Shoichet BK*, Distefano MD.* Prediction & evaluation of protein farnesyltransferase inhibition by commercial drugs. J Med Chem 53, 2464-71 (2010) PMID:20180535

111. Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA. Structure-based discovery of A2A adenosine receptor ligands. J Med Chem. 53, 3748-55 (2010). PMID: 20405927

112. Doak AK, Wille H, Prusiner SB, Shoichet BK. Colloid formation by drugs in simulated intestinal fluid. J Med Chem. 53, 4259-65 (2010) PMID: 20426472.

113. Tondi D, Calò S, Shoichet BK, Costi MP. Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors. Bioorg Med Chem Lett. 20, 3416-9. (2010) PMC3166525

114. RS Hall, AA Fedorov, R Marti-Arbona, EV Fedorov, P Kolb, JM Sauder, SK Burley, BK Shoichet, SC

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Almo & FM Raushel. The hunt for 8-oxoguanine deaminase. J Am Chem Soc.132, 1762-3 (2010). 115. Ferreira RS, Simeonov A, Jadhav A, Eidam O, Mott BT, Keiser MJ, McKerrow JH, Maloney DJ, Irwin

JJ, Shoichet BK. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors J Med Chem. 53 4891-905 (2010) PMC2895358.

116. MM Mysinger, BK Shoichet. Rapid Context-Dependent Ligand Desolvation in Molecular Docking. J. Chem. Inf. Modeling 50, 1561-73 (2010).

117. O Eidam, C Romagnoli, E Caselli, K Babaoglu, DT Pohlhaus, J Karpiak, R Bonnet, BK Shoichet* & Fabio Prati.* Design, Synthesis, Crystal Structures, and Antimicrobial Activity of Sulfonamide Boronic Acids as β-Lactamase Inhibitors J. Med. Chem. 53, 7852-63. (2010). PMC3166525

118. PN Yadav, AI Abbas, MS Farrell, V Setola, N Sciaky, XP Huang, WK Kroeze, LK Crawford, DA Piel, MJ Keiser, JJ Irwin, BK Shoichet, ES Deneris, J Gingrich, SG Beck, BL Roth. The presynaptic component of the serotonergic system is required for clozapine's efficacy. Neuropsychopharmacology. 36, 638-51 (2011).

119. SS Kamat, H Fan, JM Sauder, SK Burley, BK Shoichet, A Sali, * FM Raushel. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 133, 2080-3. (2011).

120. G Poncet-Montange, SJ St Martin, OV Bogatova, SB Prusiner, BK Shoichet, S Ghaemmaghami. A Survey of Antiprion Compounds Reveals the Prevalence of Non-PrP Molecular Targets. J Biol Chem. 286, 27718-28 (2011). PMID: 21610081

121. A Schlessinger, E Geier, H Fan, JJ Irwin, BK Shoichet, KM Giacomini & A Sali. Structure-based discovery of drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci. 108, 15810-15815 (2011). PMC3179104

122. J Carlsson, RG Coleman, V Setola, JJ Irwin, H Fan, A Schlessinger, A Sali, BL Roth*, BK Shoichet*. Comparing Structure-based Ligand Discovery from a Homology Model and the Crystal Structure of the Dopamine D3 Receptor. Nature Chem. Biol. 7, 769-778 (2011).

123. H Fan, D. Schneidman-Duhovny, JJ Irwin, G Dong, BK Shoichet & A Sali. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 51, 3078-92 (2011).

124. C Laggner, D Kokel, V Setola, A Tolia, H Lin, JJ Irwin, MJ Keiser, DL Minor, BL Roth,* RT Peterson*

& BK Shoichet*. Chemical Informatics and Target Identification in a Zebrafish Phenotypic Screen. Nature Chem. Biol., 8, 144-146 (2012).

125. MM Mysinger, DR Weiss, JJ Ziarek, S Gravel, AK Doak, J Karpiak, N Heveker, BK Shoichet*, BF Volkman* Structure-based Ligand Discovery for Chemokine Receptor CXCR4. PNAS 109, 5517-22 (2012).

126. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem. 55, 6582-94 (2012).

127. Owen SC, Doak AK, Wassam P, Shoichet MS, Shoichet BK. Colloidal aggregation affects the efficacy of anticancer drugs in cell culture. ACS Chem Biol. 7, 1429-35 (2012)

128. E. Gregori-Puigjané, V. Setola, J Hert, BC Crews, JJ Irwin, Eugen Lounkine|, Larry Marnett, BL Roth* & BK Shoichet* Identifying Mechanism-of-Action Targets for Drugs and Probes. PNAS 109, 11178-83 (2012).

129. E Lounkine†, MJ Keiser†, S Whitebread, D Mikhailov, J Hamon, J Jenkins*, P Lavan, E Weber, AK Doak, S Côté, BK Shoichet* & L Urban* Large Scale Prediction and Testing of Drug Activity on Side-Effect Targets. Nature 486, 361-7 (2012). PMID: 22722194

130. Merski M & Shoichet BK. Engineering a model protein cavity to catalyze the Kemp elimination. Proc Natl Acad Sci 109, 16179-83 (2012). PMID: 22988064

131. Eidam O, Romagnoli C, Dalmasso G, Barelier S, Caselli E, Bonnet R, Shoichet BK, Prati F.

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Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proc Natl Acad Sci 109, 17448-53 (2012). PMC3491531

132. Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK,* Raushel FM.* Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc. 135, 795-803 (2013). PMID: 23256477

133. H Lin, MF Sassano, BL Roth* and BK Shoichet*. A Pharmacological Organization of G Protein-coupled Receptors. Nature Methods 10, 140-6 (2013). PMID: 23291723

134. Sassano MF, Doak AK, Roth BL, Shoichet BK. Colloidal aggregation causes inhibition of g protein-coupled receptors. J Med Chem. 56, 2406-14 (2013). PMID: 23437772

135. Merski M, Shoichet BK. The Impact of Introducing a Histidine into an Apolar Cavity Site on Docking and Ligand Recognition J Med Chem. 56, 2874-84 (2013) PMID: 23473072

136. Cameron RT, Coleman RG, Day JP, Yalla KC, Houslay MD, Adams DR, Shoichet BK, Baillie GS. Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). Biochem Pharmacol. 85, 1297-305 (2013) PMID: 23473803

137. Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor. ACS Chem Biol. E-pub ahead of press (March, 2013). PMID: 23485065

138. Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK. Muscarinic Receptors as Model Targets and Antitargets for Structure-Based Ligand Discovery. Mol Pharmacol. 84, 528-540 (2013). PMID: 23887926

139. Benod C, Carlsson J, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EP, Fletterick RJ. Structure-based discovery of antagonists of nuclear receptor LRH-1. J Biol Chem 288, 19830-44 (2013). PMC3707686

140. Barelier S, Boyce SE, Fish I, Fischer M, Goodin DB, Shoichet BK. Roles for ordered and bulk solvent in ligand recognition and docking in two related cavities. PLoS One. 8:e69153 (2013) PMC3715451

141. GJ Rocklin, SE Boyce, M Fischer, I Fish, DL Mobley, BK Shoichet, KA Dill. Blind prediction of charged ligand binding affinities in a model binding site. J. Mol. Biol. 425, 4569-83 (2013). PMID 23896298

142. Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-Guided Discovery of New Deaminase Enzymes. J. Am. Chem. Soc. 135(37):13927-33 (2013). PMC3827683

143. AM Goble, R Toro, X Li, A Ornelas, H Fan, S Eswaramoorthy, YV Patskovsky, B Hillerich, R D Seidel, A Sali, BK Shoichet, SC Almo, S Swaminathan, ME Tanner, FM Raushel. Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes. Biochemistry, 52, 6525-36. (2013). PMC3813303

144. Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One. 8(10):e75992 (2013). PMC3787967

145. Lemieux GA, Keiser MJ, Sassano MF, Laggner C, Mayer F, Bainton RJ, Werb Z, Roth BL, Shoichet BK*, Ashrafi K.* In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding. PLoS Biol. 11:e1001712 (2013). PMC3833878

146. SC Owen, AK Doak, AN Ganesh, L Nedyalkova, CK McLaughlin, BK Shoichet* and MS Shoichet.* Colloidal Drug Formulations Explain “Bell-Shaped” Concentration-Response Curves. ACS Chem. Biol., 2014. PMC3787967

147. M Fischer, RG Coleman, JS Fraser* & BK Shoichet*. Incorportation of protein flexibility &

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conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry 6, 575-83 (2014). PMCID: PMC4144196

148. GQ Dong, S Calhoun, H Fan, C Kalyanaraman, MC Branch, S Mashiyama, N London, MP Jacobson, PC Babbitt, BK Shoichet, RN Armstrong, A Sali. Prediction of substrates for glutathione transferases by covalent docking. JCIM Epub ahead of print (2014). PMC–In progress with journal.

149. S Barelier, JA Cummings, AM Rauwerdink, DS Hitchcock, JD Farelli, SC Almo, FM Raushel*, KN Allen*, BK Shoichet*. Substrate Deconstruction and the non-Additivity of Enzyme Recognition. J. Am. Chem. Soc, 136, 7374-82 (2014). PMC4046767

150. S Barelier, O Eidam, I Fish, J Hollander, F Figaroa, R Nachane, JJ Irwin, BK Shoichet*, GD Siegal* Increasing chemical space coverage by combining empirical and computational fragment screens. ACS chemical biology 9, 1528-35 (2014). PMC4215856

151. P Avasthi, M Onishi, J Karpiak, R Yamamoto, L Mackinder, MC Jonikas, WS Sale, B Shoichet, JR Pringle, WF Marshall. Actin Is Required for IFT Regulation in Chlamydomonas reinhardtii. Current Biology. 2014/8/21.

152. M Korczynska, DF Xiang, Z Zhang, C Xu, T Narindoshvili, SS Kamat. Functional Annotation and Structural Characterization of a Novel Lactonase Hydrolyzing d-Xylono-1, 4-lactone-5-phosphate and l-Arabino-1, 4-lactone-5-phosphate. Biochemistry 53, 4727-4738 (2014).

152. N London, RM. Miller, S Krishnan, K Uchida, JJ Irwin, O Eidam, L Gibold, P Cimermančič, R Bonnet, BK Shoichet*, J Taunton* Covalent Docking of Large Libraries for the Discovery of Chemical Probes. Nature Chem. Biol. 10, 1066-72 (2014). PMID: 25344815

153. Tondi D, Venturelli A, Bonnet R, Pozzi C, Shoichet BK, Costi MP*. Targeting class A and C serine β-lactamases with a broad-spectrum boronic acid derivative. J Med Chem. 57, 5449-58 (2014). PMC4079326

154. N London, JD Farelli, SD Brown, C Liu, H Huang, M Korczynska, NF Al-Obaidi, PC Babbitt, SC Almo, KN Allen*, BK Shoichet*. Covalent docking predicts substrates for haloalkanoate dehalogenase superfamily phosphatases. Biochemistry, 54, 528-37 (2015). PMC4303301

155. D Duan, AK Doak, L Nedyalkova, BK Shoichet. Colloidal Aggregation and the in Vitro Activity of Traditional Chinese Medicines. ACS Chem Biol. 2015 Feb 9. PMID: 25606714

156. Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. PNAS 112, 5039-44 (2015). PMC4413287

157. Fischer M, Shoichet BK, Fraser JS.* One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Chembiochem. 16, 1560-4. (2015). PMC4539595

158. Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Héroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK*, Kiessling LL.* Virtual Screening for UDP-Galactopyranose Mutase Ligands Identifies a New Class of Antimycobacterial Agents. ACS Chem Biol. [ Epub ahead of print]

159. Irwin JJ*, Duan D, Torosyan H, Doak AK, Ziebart KT, Sterling T, Tumanian G, Shoichet BK*. An Aggregation Advisor for Ligand Discovery. J Med Chem. [Epub ahead of print] (Aug 21, 2015).

160. Yee SW, Lin L, Merski M, Keiser MJ, Gupta A, Zhang Y, Chien HC, Shoichet BK, Giacomini KM.* Prediction and validation of enzyme and transporter off-targets for metformin. J Pharmacokinet Pharmacodyn. 42, 463-75 (2015).

161. Pimentel-Elardo SM, Sørensen D, Ho L, Ziko M, Bueler SA, Lu S, Tao J, Moser A, Lee R, Agard D, Fairn G, Rubinstein JL, Shoichet BK, Nodwell JR.* Activity-independent discovery of secondary metabolites using chemical elicitation & cheminformatic inference. ACS Chem Biol 10, 2616-23 (2015)

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162. Barelier S, Sterling T, O'Meara MJ, Shoichet BK.The Recognition of Identical Ligands by Unrelated Proteins. ACS Chem Biol. 10, 2772-84 (2015).

163. Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA.* Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 58, 8285-91 (2015).

164. XP Haung, J. Karpiak, WK Kroeze, et al, BK Shoichet* & BL Roth*. Allosteric ligands for the pharmacologically dark receptors GPR68. Nature 527, 477-83 (2015).

165. Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U*, Shoichet BK*, Fujimori DG.* Docking & Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem. 59, 1580-98 (2016)

166. McLaughlin CK, Duan D, Ganesh AN, Torosyan H, Shoichet BK*, Shoichet MS*. Stable Colloidal Drug Aggregates Catch and Release Active Enzymes. ACS Chem Biol. (Jan 15, 2016).

167. Farrell MS, McCorvy JD, Huang XP, Urban DJ, White KL, Giguere PM, Doak AK, Bernstein AI, Stout KA, Park SM, Rodriguiz RM, Gray BW, Hyatt WS, Norwood AP, Webster KA, Gannon BM, Miller GW, Porter JH, Shoichet BK, Fantegrossi WE, Wetsel WC, Roth BL. In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. PLoS One. 11(3):e0150602. (2016)

168. A Manglik, H Lin2, et al., BK Kobilka*, P Gmeiner*, BL Roth*, & BK Shoichet2*. Structure-based discovery of biased μ-opioid receptor analgesics with reduced side effects. Nature, Aug 17, 2016

Perspectives & Commentaries (5) 1. BK Shoichet. Virtual Screening of Chemical Libraries. Nature, 432, 40-43 (2004).

2. AR Leach, BK Shoichet & CE Peishoff*. Docking and scoring: successes and gaps. J Med Chem. 49, 5851-5 (2006).

3. MJ Keiser, JJ Irwin & BK Shoichet. The chemical basis of pharmacology. Biochemistry 49, 10267-762010 (2010).

4. BK Shoichet & BK Kobilka. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci.; 33, 268-72 (2012).

5. BK Shoichet. Drug Discovery: Follow your lead. Nature Chemical Biology 10, 244-245 (2014). Book Chapters 1. Shoichet, B.K.*, Docking ligands to proteins, Protein Structure Prediction, A Practical Approach,

IRL Press, M.L. Sternberg, ed., Oxford (1996).

2. BK Shoichet. The organization & identification of Ligand Binding Sites on Proteins, Computer Assisted Modeling in Molecular Pharmacology, Marcel Dekker, PS Charifson ed. New York, 1997.

Review Articles (11) 1. ID Kuntz, EC Meng & BK Shoichet, Structure-Based Drug Design, Accounts of Chemical

Research, 27, 117-123 (1994)

2. ID Kuntz, EC Meng & BK Shoichet, Challenges in Structure-Based Drug Design, New Perspectives in Drug Design, 137-153, (1995).

3. BK Shoichet.* & ID Kuntz*; "Predicting the Structures of Protein Complexes: A Step in the Right Direction, Chemistry & Biology 3, 151-156 (1996).

4. BK Shoichet & DE Bussiere*; Macromolecular Crystallography and Lead Discovery: Possibilities and Limitations. Current Opinion in Drug Discovery 3, 408-422 (2000).

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5. Shoichet, B.K.*, McGovern, S.L., Wei, B., Irwin, J.J. Lead Discovery Using Molecular Docking. Current Opinion in Chemical Biology, 6, 439-446 (2002).

6. BK Shoichet. Screening in a Spirit-Haunted World. Drug Discovery Today 11, 607-615 (2006).

7. Feng BY, Shoichet BK. A detergent-based assay for the detection of promiscuous inhibitors. Nature Protocols 1, 550-3 (2006).

8. Kolb P, Ferreira RS, Irwin JJ, Shoichet BK. Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol. 20, 429-36. (2009).

9. Keiser MJ, Irwin JJ, Shoichet BK*. The chemical basis of pharmacology. Biochemistry 49,10267-76 (2010).

10. Shoichet BK, Kobilka BK. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci. 33, 268-72. (2012).

11. Irwin JJ, Shoichet BK. Docking screens for novel ligands conferring new biology. J Med Chem. 2016 Feb 25. [Epub ahead of print]. PMID: 26913380

Inventions Patents 2000 GS Weston & BK Shoichet. Inhibitors of β-lactamases and uses therefor. US 6075014

2001 GS Weston & BK Shoichet. Inhibitors of β-lactamases and uses therefor. US 6184363

2002 BK Shoichet & GS Weston. Inhibitors of β-lactamases and uses therefor. US 6417174

2002 BK Shoichet & GS Weston. Inhibitors of β-lactamases and uses therefor. US 6448238

2001 (pending) Shoichet, B.K., Caselli, D., Prati, F., Blaszczak, L.C., Acylaminomethyl Boronic Acid Inhibitors of Serine β-lactamases to Reverse Bacterial Resistance to β-lactam Antibiotics. Full patent filed with USPO Sept 2001.

2005 Shoichet, B.K. & McGovern, S.L., Methods of identifying non-specific inhibitors of biomolecule . US 6,887,658 (Published 05/03/2005, filed 06/14/2002).

2007 Shoichet, B.K. & Prati F., Nanomolar β-lactamase inhibitors . US 7,928,129 4/19/11

2009 Shoichet, B.K. & Powers, R.P., Non-covalent inhibitors of AmpC β-lactamase. US 7,541,381 B2

2005 (pending) Howard, Laurence; Miller, Steven; Irwin, JJ & Shoichet, BK. Compositions and methods for altering immune function. U.S. Provisional Patent Application 60/686,224, filed June 1, 2005 and prosecuted May 31, 2006.

2011 (pending) O Eidam C Romagnelli, E Caselli, F Prati & BK Shoichet. Sulfonamide boronic acid inhibitors of β-lactamase. U.S. Provisional Patent Application filed.

2015 (pending) Provisional 62/190,390 Mu Opioid Receptor Modulators Copyrighted Programs 1991 Shoichet, B.K. & Kuntz, I.D.; DOCK2.0, Program and Manual, UC Regents.

1992 Meng, EC, Shoichet, BK & Kuntz, ID; DOCK3.0, Programs and Manuals, UC Regents.

1994 Meng, EC, Shoichet, BK & Kuntz, I.; DOCK3.5, Programs and Manuals, UC Regents.

2000 Lorber, D.A. & Shoichet, B.K.; DOCK3.5.ens. Program. Northwestern University.

2007 Keiser MJ & Shoichet BK; SEA Program & Manual. UC Regents.

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Research Grants/Contracts Current (annual adjusted direct costs to Shoichet lab)

National Institutes of Health R01 GM59957 (Shoichet, PI) 8/1/99 – 11/30/13 Design and experimental testing of new docking methods. $212,500/yr

National Institutes of Health R01 GM071630 (B Shoichet PI, M Shoichet Co-I) 8/01/04 – 02/29/16 A Specific Mechanism of Non-Specific Inhibition $207,000/yr

National Institutes of Health R01 GM71896 (Shoichet, PI) 08/01/04 – 05/31/16 A Web-Based Automatic Molecular Docking System $212,500

National Institutes of Health P01 GM106990 (PI: Brian Kobilka) 09/01/13 – 08/31/18 Structure-based discovery of allosteric ligands for G Protein Coupled Receptors $190,000/yr Shoichet is PI on Project 1 of this four group program project.

FDA CERSI Sub Award (PI: K. Giacomini) 04/01/15 – 03/31/16 Target Identification for Excipients $260,000/yr

NIH Office of the Director (PI: BL Roth) 08/01/14 – 07/31/17 Illuminating the Druggable GPCRome $135,000/yr Past (total direct costs) PhRMA Foundation (Shoichet, B.K., PI) 1/1/96 – 12/31/97 Research Starter Grant $25,000

PRF of the Amer. Chem. Soc. (Shoichet, B.K., PI) 9/1/96 – 8/31/98 Catalysis in Thermophilic Enzymes $20,000

Howard Hughes Medical Institute (Larry Jameson, PI) 1/1/97 – 12/31/98 Faculty Development Grant $75,000

PhRMA Foundation (Shoichet, B.K., PI) 7/1/97 – 6/30/99 Faculty Development Award $60,000

Pharmacia Pharmaceuticals. (Shoichet, B.K., PI) 6/15/99 – 8/31/01 Screening a Database Using Molecular Docking $134,922

The Animal Alternative Program of Procter & Gamble (Shoichet, PI) 3/1/97 – 2/28/01 Developing Computer Models of Drug Action $145,000

Genetics Institute (Shoichet, B.K., PI) 2/1/98 – 12/31/00 Database Screening by Molecular Docking $92,000

Procter & Gamble Pharmaceuticals. (Shoichet, B.K., PI) 10/1/97 – 03/01/02 Docking for novel and improved inhibitors $254,841

Consensus Pharmaceuticals. (Shoichet, B.K., PI) 10/1/99 – 10/31/00 Screening a Database Using Molecular Docking $47,620

Howard Hughes Medical Institute (Shoichet, B.K., PI) 8/1/00 – 7/31/02 Medical Student Research Fellowship for Indi Trehan $58,000

American Chemical Society (Shoichet, B.K., PI) 9/1/01 – 8/31/02 Med. Chem. Predoctoral fellowship for Rachel Powers $20,000

National Science Foundation (Shoichet, B.K., PI) CAREER MCB-9734484 3/1/98 – 2/28/03 Identifying Ligand Binding Sites in Proteins $312,925

Eli Lilly & Co. (Shoichet, B.K., PI) 9/1/97 – 06/30/02 Characterizing non-ß-lactam inhibitors of β-lactamases $235,272

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Pharmacia Corporation (Shoichet, B.K. PI) 09/1/02 – 08/31/03 Promiscuous Inhibitors $112,000

PhRMA Foundation (Shoichet, B.K., PI) 7/1/01 – 6/30/03 Research Fellow in Clinical Pharmacology for Susan McGovern $12,000

Howard Hughes Medical Institute (Shoichet, B.K., PI) 8/1/00 – 7/31/02 Medical Student Research Fellowship for Tomer Roth $32,000

UC Discovery bio03-10401 (D. Agard, PI) 09/1/04 – 08/31/05 Structure-based discovery of Hsp90 inhibitors $50,000

QB3 award (Shoichet/Guy) 01/01/04-12/31/05 Fundamental Determinants of False Positives in HTS $60,000

National Institutes of Health R03 DA024891 (Shoichet, PI) 08/01/07 – 07/31/08 High Throughput and Virtual Screens for new cruzain inhibitors $16,000/yr

Fight for Mike (Shoichet) 07/01/07-06/30/09 Docking for Inhibitors of PrP. $172,000/yr

Rogers Bridging the Gap (Shoichet, PI) 12/01/08-11/30/11 An Automated System for Inhibitor Discovery $112,500/yr

National Institutes of Health U54 GM072970 (R. Altman, PI) 09/01/10 – 08/31/13 Simbios Collaborative Center Grant $60,000/yr

National Institutes of Health P01 GM71790 (J. Gerlt, PI) 08/01/04 – 07/31/14 Deciphering Enzyme Specificity $93,000/yr

National Institutes of Health P01 AG02132 (S. Prusiner, PI) 01/01/09 – 01/31/14 Degenerating & Dementing Diseases of Aging $65,000/yr

National Institutes of Health U54 GM093342 (J. Gerlt, PI) 05/01/10 - 04/30/15 Collaborative Center For An Enzyme Function Initiative $170,000/yr

National Science Foundation CHE-1223785 (B. Kobilka, PI) 09/01/12 – 05/31/15 International Collaboration in Chemistry: The Chemical Basis for Allosteric $30,000/yr Regulation of Muscarinic GPCRs National Institutes of Health R01 GM63815 (Shoichet, PI) 8/1/01 – 3/31/14 Structure, Function & Inhibition of β-lactamases $200,000/yr Invited Seminars (315 total) International Symposia & Seminars (71) 1. Drug Information Association: Computer-Based Drug Design, Montreux Switzerland, October 1993.

Structure-Based Inhibitor Discovery Using DOCK.

2. International Union of Biochemistry and Molecular Biology Annual Meeting, Singapore, April 1995. Probing Proteins for Ligand Binding Sites.

3. Chemical Lead Generation in Drug Discovery, Society of Chemical Industry, Cambridge England, June 1995. Structure-Based Inhibitor Design: Novel Ligands, Novel Binding Sites.

4. Novo Nordisk Copenhagen Denmark, June 1995. A relationship between protein stability & function

5. Lepetit Research Center, Milan Italy, June 1995. Structure-Based Inhibitor Design: Novel Ligands, Novel Binding Sites.

6. Proteus Pharmaceuticals Inc., Macclesfield UK, June 1995. Structure-Based Inhibitor Design: Novel Ligands, Novel Binding Sites.

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7. Structure-based Design; NATO School. Erice Italy, June 1996. Solvation and Conformation in Structure-based Inhibitor Discovery.

8. Structure-based Design; NATO School. Erice Italy, June 1996. A Relationship Between Protein Stability and Protein Function.

9. University of Alberta, Dept. of Biochemistry, Edmonton, Alberta. July 1996. A Relationship Between Protein Stability and Protein Function.

10. University of Modena, Dept. of Chemistry, Modena Italy. June 1998. Structure-Based Inhibitor Design Against β-lactamases.

11. Boeringer-Ingelheim, Montreal Canada, Oct 2001. Structure-based inhibitor discovery using molecular docking.

12. AstraZeneca, Moldenal Sweden, Dec. 2001. Hits, leads, and artifacts from screening

13. AstraZeneca, Manchester England, Dec. 2001. Hits, leads, and artifacts from screening

14. Bioinformatics Symposium, National Taiwan Normal University, Taipei Taiwan. Feb 18 2002. Introduction to Molecular Docking: Sampling, Scoring, & Simple Systems.

15. Bioinformatics Symposium, National Taiwan Normal University, Taipei, Feb 19 2002. Screening Databases for Lead Discovery I: The Problem of False-Positives.

16. Bioinformatics Symposium, National Taiwan Normal University, Taipei, Feb 20 2002. Screening Databases for Lead Discovery II: Applications to Pharmaceutical Targets.

17. Molecular Informatics: Confronting Complexity, Bielstein-Institut, Bozen Italy, May 13th-16th, 2002, Hits, Leads, and Artifacts from Molecular Docking & Other Screens.

18. University of Modena, Modena Italy, May 2002. Structure, function, & inhibition of β-lactamases.

19. From Genes to Drugs through Crystallography, NATO Summer School, Erice Italy, May 2002. Hits, Leads, and Artifacts from Virtual & High Throughput Screening.

20. Univ. of Toronto, Canada 08/02. Hits, leads, & artifacts from virtual & high throughput screening.

21. International Symposium on Chemical Informatics, Seoul Korea May 20-22, 2003. Model Systems for Molecular Docking.

22. ISQBP President's meeting, Como Italy June 2004. Model systems for molecular docking.

23. ETH, Lausanne Switzerland June 2004. Model systems for molecular docking.

24. AstraZeneca, Montreal Canada Oct 2004. A specific mechanism for non-specific inhibition.

25. Astra Lectureship, University of Ottawa, Ottawa Canada Oct 2004. Model systems for molecular docking. [email protected]

26. Boeringer Ingelheim, Germany April 2005 Model systems for molecular docking. [email protected]; [email protected]

27. Boeringer Ingelheim, Germany April 2005. A specific mechanism for non-specific inhibition.

28. 8th Annual Symposium of Canadian Society for Pharmaceutical Sciences, Toronto Canada. May 2005. Model Systems for Molecular Docking. [email protected].

29. International Molecular Graphics and Modelling Society, Dublin Ireland (Trinity College Dublin) September 2005. Model Systems for Molecular Docking. David Lloyd, [email protected]

30. Boeringer-Ingelheim, Montreal Canada, Nov 2005. Structure-based virtual screening. [email protected]

31. International Molecular Graphics & Modeling Society Meeting, Perth, Australia. April 2006. Docking to Model Binding Sites. Plenary Speaker. Ricardo Mancera [email protected]

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32. XIXth International Symposium on Medicinal Chemistry, Istanbul Turkey Aug 2006. “Structure-based virtual screening & chemical information.” http://www.ismc-2006.org.

33. Novartis Chemistry Lectureship, Basel Switzerland. Structure-based screening & chemical information. Dec 10, 2006. [email protected]

34. Novartis Chemistry Lectureship, Vienna Austria. Structure-based screening & chemical information. Dec 2006.

35. Therapeutic Applications of Computational Biology and Chemistry, Cambridge UK. “Interrogating Target Function & Recognition Through Ligand Chemistry. March 2007. [email protected].

36. Novartis Chemistry Lectureship, Horsham UK. March 2007 [email protected]

37. Reischoltzhausen Meeting: Merging Chemical & Biological Space, Marburg Germany. March 2007. Relating Protein Pharmacology by Ligand Chemistry.

38. Novartis Chemistry Lectureship, Tsukuba Japan. A specific mechanism for non-specific inhibition. [email protected]. April 2007.

39. Welcome Trust Meeting on Structural Genomics, London England, Dec 10 2007. Substrate and inhibitor prediction from protein structure.

40. 3eme Cycle en Chemie: University of Berne, Berne Switzerland, May 5 2008. Docking vs. Screening vs. The Creature from the Black Lagoon. Jean-Louis Reymond.

41. 3eme Cycle en Chemie: University of Berne, Berne Switzerland, May 6 2008. Forward and Reverse Chemical Information in Biology Jean-Louis Reymond.

42. 3eme Cycle en Chemie: University of Friborg, Friborg Switzerland, May 7 2008. Predicting Substrates for Targets and Targets for Drugs.

43. 3eme Cycle en Chemie: University of Berne, Lausanne Switzerland, May 8 2008. Predicting Protein Pharmacology by Ligand Chemistry.

44. 3eme Cycle en Chemie: University of Berne, Geneva Switzerland, May 9 2008. Predicting New Biology from Chemical Information.

45. From genes to drugs through crystallography, NATO School, Erice Italy, May-June 2008.

46. 33rd FEBS Congress/11th IUBMB on Biochemistry of Cell Regulation. Athens Greece. Hits, leads and artifacts from virtual and high-throughput screening. June-July, 2008. Nikos Oikonomakos <[email protected]>

47. 2nd SCI/RSC meeting on Medicinal Chemistry of GPCRs, Gothenburg Sweden. Predicting Off-Target Effects & Polypharmacology. Sept 8-10 2008. [email protected]

48. EMBO Symposium: Protein Design & Evolution for Biocatalysis. Costa Brava, Spain. Forward & Reverse Chemical Information in Biology. Oct 25-30, 2008. Jiri Damborsky.

49. Ontario Cancer Research Symposium on Chemical Biology, Toronto Canada. New Leads for Old Targets and New Targets for Old Drugs. Nov 10, 2008. [email protected]

50. Frontiers of the Pharmaceutical Sciences Symposium, Toronto Canada. Why should high-

throughput screening ever work? May 28-29 2009. [email protected] [email protected] .

50. Pasteur Institute, Paris France. New ligands for old targets and new targets for old drugs. Michael Nilges, [email protected]. June 10, 2009.

51. Basel Chemical Society Lectures, Basel Switzerland. A Chemical View of Pharmacological Networks. [email protected]. June 11, 2009.

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52. Fragment-Based Lead Discovery, York England. Docking for fragments: hit-rates, structures and chemical space. Rod Hubbard. [email protected]. Sept 21-23, 2009.

53. Centre for Protein Science and Crystallography, Structure-based discovery & design. Hong Kong China. Dec 2009. [email protected] (Pang-Chui Shaw).

54. Pfizer, Sandwich UK. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space. June 1, 2010.

55. GlaxoSmithKline, Stevenege UK. Chemical interrogation of pharmacological networks. 06/02/2010

56. UCB Pharma, Brussels, Belgium. Chemical interrogation of pharmacological networks 06/14/2010

57. Univ of Leiden, Netherlands. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space. June 15, 2010.

58. Great Lakes GPCR Retreat, King City Canada. New ligands for old targets and new targets for old drugs. Oct 21-23, 2010. [email protected]>

59. Ontario Cancer Institute, Toronto Canada. A Chemical Lens on Pharmacological Networks. Nov 4, 2010. Rob Rottapel, Donna Defrancesco [email protected]

60. ZING Structural Biology and Drug Discovery. Riviera Maya, Mexico. New ligands for old targets and new targets for old drugs. Dec 4-7, 2010.

61. National Institute for Biomedical Science (NIBS), Beijing China. New ligands for old targets and new targets for old drugs. June 14, 2011.

62. Shanghai Institute of Materia Medica, Shanghai China. The chemical basis of pharmacology. June 17, 2011.

63. Cellular Dynamics of Macromolecular Complexes, Montreal Canada. Structure-based ligand discovery for G-Protein Coupled Receptors. June 22-23, 2011. [email protected]

64. 3rd European Chemical Biology Conference, Vienna Austria. Chemical Networks in Pharmacology (or De-Orphanizing the GPCR-ome). July 1-3, 2012. Riki Eggert.

65. Chemical Biology 2012, Heidelberg, Germany. Chemical Networks in Pharmacology (or De-Orphanizing the GPCR-ome). Sept, 2012. John Overington.

66. 7th International Meeting on the Molecular Pharmacology of GPCRs. Melbourne Australia. Backwards and Forwards with Structural and Classical Pharmacology. Dec 6-8 2012. [email protected]

67. 7th Noordwijkerhout Symposium on Pharmacokinetics, Pharmacodynamics and Systems Pharmacology. Noordwijkerhout, Netherlands. Chemical integration of the time domain in molecular signaling networks. April 23-25, 2014. [email protected].

68. International Chair of Therapeutic Innovation, CNRS, Paris France. “A Metabolic Code for Cell Signaling”. Jan 13 & Jan 14, 2015. [email protected]. Rodolphe Fischmeister.

69. Molecular Graphics & Modeling Society, Friedrichs Alexander University, Germany. “A metabolic code for cell signaling. Tim Clarke. Plenary Lecture. April 5, 2016.

70. GLISTEN Network for GPCRs, Erlangen Germany. A cure for pain. April 6-9, 2016. Peter Gmeiner.

National Symposia (USA & Canada) (72) 1. Molecular Graphics Society, Albuquerque NM, May 1993. A Practical Guide to DOCK.

2. Structure-Based Drug Design Meeting, IBC, San Diego CA, December 1994. Structure-Based Inhibitor Discovery against T4 Lysozyme and Thymidylate Synthase.

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3. Constrained and Structural Libraries Conference, IBC, Philadelphia PA, March 1995. Not Just Conformation: Configuration Can Vary Too.

4. Bioorganic Gordon Conference, Andover, NH. June 1997. Structure-Based Inhibitor Discovery Against β-Lactamases.

5. Data Management for Drug Discovery & Design, IBC, San Francisco CA, June 1997. Structure-Based Discovery of Novel Inhibitors from Molecular Databases.

6. National Managed Health Care Congress, Washington DC. September, 1997. Structure-Based Design and Combinatorial Elaboration of Novel Inhibitors of Thymidylate Synthase.

7. Computers in Combinatorial Chemistry, American Chem. Soc. National Meeting, Anaheim, CA March, 1999. Molecular Docking Algorithms in Database Screens.

8. SuperComputing ’99, Portland OR, 11/99. The docking problem in biology & inhibitor discovery.

9. American Soc. for Tropical Med. & Hygiene, Houston TX, Oct. 2000. Structure-based inhibitor discovery.

10. Computational Structural Biology Symposium, Tallahasse FL, Jan 2001. Distinguishing Among Docking Fits in Simple and Complex Interfaces.

11. Structure-Based Drug Design Conference (CHI), Cambridge MA, April 2001. Development & Experimental Testing of New Docking Methods.

12. American Society for Microbiology Natl. Meeting, Orlando FL, May 2001. Structure, Function, & Inhibition of AmpC β-lactamase.

13. Modeling Of Protein Interactions In Genomes, Charlotte SC. June 16-19 2001. Docking protein ligands in multiple conformations with strict energy functions.

14. Bioorganic Gordon Conference, Plymouth NH. June 20, 2001. Stability as a Constraint on the Function & Evolution of a Resistance Enzyme,

15. QSAR Gordon Conference, Tilton NH, Aug 2001. Hits, Leads, and Artifacts from Molecular Docking & Other Screens.

16. Docking & Scoring Session, American Chemical Society National Meeting, Chicago, IL Aug 2001. Hits, Leads, and Artifacts from Molecular Docking & Other Screens.

17. 6th Annual Meeting on Molecular Diversity. Lake Tahoe CA, Jan 2002. Hits, leads, & artifacts from screening,

18. Physical Chemistry Session, ACS National Meeting, Orlando, April 2002. The Null Hypothesis in Molecular Docking.

19. Lifetime Achievement Award Session for Irwin Kuntz, ACS National Meeting, Orlando, April 2002. Structure, Function & Inhibition of β-lactamase.

20. Aventis Chemical Biology Company-wide Symposium, ATT Center NJ, June 2002. Hits, Leads, & Artifacts from Virtual & High-Throughput Screening

21. Medicinal Chemistry Session, ACS National Meeting, New Orleans, March 2003. A mechanism for promiscuous inhibition & its occurrence among hits, leads, & drugs.

22. Computational Chemistry Session, ACS National Meeting, New Orleans, March 2003. Exploring protein flexibility in a model docking system.

23. Drug Design by Target Class, Strategic Research Institute, San Francisco CA, June 2003. Hits, leads, and artifacts from virtual & high-throughput screening.

24. Enzymes Gordon Conference, NH USA 07/2003. A specific mechanism for non-specific inhibition.

25. Symposium on Computational Modeling and Solvation in Drug Discovery Protein Society, Boston, July 26, 2003. Model Systems for Molecular Docking.

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26. Symposium on Protein Bioinformatics: Domains, Docking, and Dynamics Protein Society, Boston, July 26, 2003. Docking vs. Screening vs. The Creature from the Black Lagoon.

27. Society for Biological Screening National Meeting, Portland OR, 09/21-25/03. A specific mechanism for non-specific inhibition. [email protected]

28. NIGMS Workshop on High-Accuracy Comparative Modeling, Bethesda MD, Oct 2003. Docking to holo, apo, and modeled structures.

29. Reversible Associations In Structural & Molecular Biology Gordon Conference, Venture CA, Jan 2004. Model Systems for Molecular Docking.

30. Keystone Symposium on New Advances in Drug Discovery, Keystone CO, A specific mechanism for non-specific inhibition. Paul Bartlett, March 21-26, 2004.

31. ACS National Meeting, Philadelphia PA. Aug 22-26 2004. Model systems for molecular docking.

32. Bioorganic Gordon Research Conference, Proctor NH. June 2005. A specific mechanism for non-specific inhibition.

33. Medicinal Chemistry Gordon Research Conference, Tilton NH. Aug, 2005. [email protected]. A specific mechanism for non-specific inhibition of screening hits.

34. 45th ICAAC, “The Antibiotic Pipeline: What's In It?", New Orleans LA. Sept 21-24, 2005. The ABCDs of Beta-Lactamase Inhibitors. [email protected]

35. 231st National ACS Meeting, Atlanta GA. March 26-28, 2006. Understanding Decoys & Hits in Molecular Docking. [email protected]

36. Keystone Symposium, Whistler, British Columbia. April, 2006. Understanding Decoys & Hits in Molecular Docking.

37. 232nd National ACS Meeting, San Francisco CA. Sept 12, 2006. Understanding Decoys & Hits in Molecular Docking.

38. AACR/ACS Joint Meeting: Chemistry in Cancer Research, San Diego CA. Feb 4-7, 2007. Virtual Screening for Structure-Based Inhibitor Discovery . Steven Hecht, U. Minn. [email protected]

39. Modern Drug Discovery & Development Summit, San Francisco, CA 11/28-30, 2007. "Differences and Complementarities between Hits and Hit Rates from Virtual & High-Throughput Screening". Rania Hafez. [email protected]

40. American Assoc of Pharmaceutical Scientists, South San Francisco, CA 05/19, 2009. "Docking vs. Screening vs. The Creature from the Black Lagoon".Jeff Silverman [email protected]

41. Keystone Symposium, Steamboad Springs, CO. 3/29-4/03, 2008. Learning from Failure in Molecular Docking.

42. ACS National Meeting, Philadelphia PA. 8/17-19, 2008. Druggability and Chemical Space in Fragment Docking. ID 1197626, Password 416205

43. ACS National Meeting, Philadelphia PA. 8/17-19, 2008. Comprehensive analysis of hits from high-throughput and docking screens.

44. CUP OpenEye Meeting, Santa Fe NM. 3/8-11/2009. Chemoinformatic and Structure-Based Screens for GPCR ligands (or, Why does screening ever work?).

45. ASBMB National Meeting, New Orleans LA. 4/18-23/2009. Predicting Drug Off-Target Effects & Polypharmacology.

46. Nature Chemical Biology Meeting, Boston MA. 9/18-20/2009. Figments, Fragments, and the Gobsmacking Emptiness of Chemical Space.

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47. ACS National Meeting, Washington DC. 8/18, 2009. Predicting the identity and affinity of ligands in model cavity sites.

48. Gordon Conference on Biomolecular Interactions and Methods, Galveston TX. 1/17-22, 2010. [email protected] Chairing/speaking in Molecular Interactions and Disease session.

49. Keystone Meeting on GPCRs, Keystone CO. April 7-12, 2010. Structure-based and chemoinformatic screens for new GPRC ligands. Brian Kobilka.

50. Quantitative & Systems Pharmacology Workshop, NIGMS Washington, DC. Sept 9-10, 2010. A chemical lens on pharmacological networks.

51. ConfometRx GPCR Workshop, Honolulu HI Dec 7-11 2010. Structure-based screens for new GPCR ligands. Brian Kobilka.

52. Society for laboratory automation & screening National Meeting, Orlando FL. March 2011. Mechanism & effects of colloidal aggregation in early discovery & pharmacology. [email protected]

53. Keystone Meeting on High-Throughput Structural Biology, Keystone CO. January 22 – 27 2012. “…that has such structures in’t”.

54. Keystone Meeting Addressing the Challenges of Drug Discovery, Granlibakken CA. March 19– 23, 2012. The Chemical basis of Pharmacology.

55. ACS National Meeting, The Chemical Basis of Pharmacology, San Diego CA. March 27, 2012.

56. Am. Assoc. of Cancer Research National Meeting, Meet the Experts Session: The Chemical Basis of Pharmacology, Chicago IL. March 31, 2012. (Ben Neel).

57. ACS National Meeting, Chemical Networks in Pharmacology, Philadelphia PA. Aug, 2012.

58. CIFAR Meeting on Genetic Networks. Backward and Forward with Molecular & Classical Pharmacology. Toronto ON. Oct 2012.

59. ACS National Meeting, Colloidal aggregates in vitro & in vivo, Indianapolis IN. 09/2013. Dan Ortwine

60. ACS National Meeting, Chemo-evolutionary basis of polypharmacology, Indianapolis IN. Sept 2013. Jeff Sutherland.

61. Quantitative & Systems Pharmacology, Chemo-evolutionary basis of polypharmacology. Univ. of Pittsburgh, Pittsburgh PA Nov 11-12, 2013. Jeremy Berg.

62. Biomacromolecules Gordon Research Conference. Chemo-evolutionary basis of polypharmacology. Salve Regina Rhode Island June 1-6 2014. Ivet Bihar.

63. Protein Society Meeting, Model Systems for Testing Docking and Affinity Methods. San Diego, CA. July 27-31, 2014.

64. Cambridge Healthtech Institute’s 10th Annual Drug Discovery Chemistry, Plenary Keynote. San Diego, CA April 21-23 2015. Anjani Shah

65. 9th Annual Chapel Hill Drug Conference, Chapel Hill NC. Keynote. A metabolic code for cell signaling. Oct 25, 2015.

66. International Light Scattering Colloquium, Wyatt Technologies, Santa Barbara CA, Plenary Keynote. Colloidal Aggregation in Drug Discovery & Pharmacology. Nov 3, 2015. Geoff Wyatt.

67. The GPCR Workshop, Kona Hawaii. Dec 1-5, 2015. Targeting New GPCR Binding Sites for New Chemotypes & New Biology

68. Keystone Meeting on GPCRs, Keystone CO. Feb 22-25, 2016. Structure-based & Network Pharmacology of GPCRs. Art Christopoulous & Laura Bohn.

69. Yale Chemical Biology Symposium. Docking for new chemotypes with new pharmacology for GPCRs. Alanna Schepartz, May 13 2016.

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70. Gordon Research Conference on Drug Safety, Stonehill College, Easton MA. July, 2016. James Stevens [email protected]. A metabolic code for cell signaling.

71. SPS/JSPS/CSPT Joint meeting, Vancouver, Canada. Sept 19, 2016. Laszlo Urban, GPCRs in pharmacology session. A cure for pain.

72. ASBMB, Chicago IL. April 22-26, 2017. [email protected]. Delano Award Letctureship. New Chemical Probes to Illuminate GPCR Pharmacology.

Regional Symposia (6) 1. West Coast Crystallography Meeting, Asilomar CA, March, 1995. A Relationship Between Protein

Structure and Protein Function.

2. Great Lakes ASPET Meeting, Chicago IL, June 1997. Structure-based inhibitor discovery vs β-lactamases.

3. ACS Central Regional Meeting, Grand Rapids MI June 2001. Structure-based inhibitor design against β-lactamase.

4. Midwest Enzymes & Chemistry Conf, Chicago Oct 2002. Structure, function & inhibition of β-lactamase.

5. Southwest American Chemical Society Meeting, Ft. Worth Texas Sept 2004. Model systems for molecular docking [email protected] Keynote address.

6. Partnership for Excellence in Structural Biology; Chemical Biology & Structure-based ligand discovery. University of Connecticut Oct 14, 2016. Sandra Weller, [email protected]. “A Cure for Pain.” Keynote address.

Seminars in the USA & Canada (167) 1. Tripos User’s Group Meeting, St. Louis MO., April 1991. Structure-Based Inhibitor Design.

2. Vertex Pharmaceuticals, Boston MA, August 1991. Structure-Based Inhibitor Design.

3. Glaxo Inc., RTP NC, April 1992. Structure-Based Inhibitor Design Against Thymidylate Synthase.

4. Chiron, Emoryville CA, November 1992. Structure-based inhibitor design vs thymidylate synthase.

5. Northwest Crystallography Meeting, Seattle WA, April 1994. A Relationship Between Protein Stability and Protein Function.

6. Techniques for Computer-Based Drug Design, Seattle WA, May 1994. Molecular Docking.

7. Chiron, Emoryville CA, November 1994. A relationship between protein stability & function.

8. University of Southern California, Department of Pharmaceutical Chemistry, Los Angeles CA, April 1995. A Relationship Between Protein Structure and Protein Function.

9. Chicago Medical School, Chicago IL, March 1996. A relationship between protein structure & protein function.

10. Dupont -Merck Computational Chemistry Series, Wilmington Delaware, March 1996. A Devil in the Details: Configuration, Conformation, and Resolution in Molecular Docking.

11. Northwestern University Dept. of Chemistry, Evanston IL, April 1996. A Relationship Between Protein Stability and Protein Function.

12. Procter & Gamble, Cincinnati OH. November, 1996. Developing Computer Algorithms for the Prediction of Biological Activity.

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13. Children’s Memorial Hospital, Chicago IL. March 1997. Design of Novel Drugs Based on Receptor Structure: Application of 3-Dimensional Modeling.

14. Bioinformatics & Drug Discovery, Evanston IL. July 1997. Structure-Based Inhibitor Discovery.

15. Genetics Institute, Boston MA, July 1997. Flexible Ligand Docking.

16. Procter & Gamble Pharaceuticals, Cincinnati OH. February, 1998. Screening for Novel Inhibitors Using Molecular Docking.

17. Wayne State University Dept. of Chemistry, Detroit MI. February 1998. Structure-Based Inhibitor Discovery Using Molecular Docking.

18. University of Chicago, Dept. of Pharmacology, Chicago IL. March, 1998. Structure-Based Inhibitor Design Against β-lactamases.

19. University of Illinois, Chicago IL. Nov 1998. Structure-based inhibitor discovery vs β-lactamases.

20. Bristol-Myers Squib, Princeton NJ. Feb 1999. Flexible ligand docking using chemical and conformational ensembles.

21. University of California, Santa Cruz, April 1999. Structure-based inhibitor design vs β-lactamase.

22. Applied Structure-Based Drug Design, UCSF, San Francisco CA, April 1999. Structure-Based Inhibitor Design Against β-lactamases.

23. PhRMA Foundation Annual Meeting, New York City, April 1999. Structure-Based Inhibitor Design Against β-lactamases.

24. Consensus Pharma, Boston MA, July 1999. Molecular docking & inhibitor discovery

25. Vertex Pharmaceuticals, Cambridge MA, July 1999. Molecular Promiscuity.

26. Abbott Pharmaceuticals, Abbott Park IL. Aug 1999. Flexibility, solvation, & diversity in docking.

27. Midwest Enzymes in Chemistry Conf, Chicago Oct 1999. Structure, function & inhibition of AmpC β-lactamase.

28. Illinois Inst. of Technology, Chicago IL. Nov 1999. Structure-based design against β-lactamase.

29. Univ. of Washington Seattle WA, 01/2000. Structure-based inhibitor discovery using molecular docking.

30. Univ. of Washington, Seattle WA, Jan 2000. Structure-based inhibitor design against β-lactamase.

31. Wesleyan University, Wesleyan CN, Feb 2000. Structure, function & inhibition of β-lactamase.

32. Southern Illinois Univ., Carbondale, April 2000. Structure, function & inhibition of β-lactamase.

33. Univ. of Illinois Bioeng., Chicago IL, Sept 2000. Structure-Based Database Screening Using Molecular Docking.

34. Phamacia, St. Louis MO, Oct 2000. Development & Testing of New Docking Methods.

35. Sunesis Pharmaceutical, San Francisco CA, Nov 3, 2000. Structure-Based Database Screening Using Molecular Docking: New Opportunities, New Problems.

36. UT Southwestern, Dallas TX, Dec 2000. Structure-based screening using molecular docking.

37. Pharmacia, Kalamazoo MI, Jan 2001. Inhibitor Discovery & Design Using Molecular Docking.

38. Eli Lilly & Co., Indianopolis IN, Feb 2001. Development & Testing of New Docking Methods.

39. OpenEye Meeting, Santa Fe NM, March 2001. Levinthal Lecture: The Problem with Docking.

40. Biogen Inc, Cambridge MA, April 2001. Screening Databases Using Molecular Docking.

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41. Univ. of Illinois Med. Chem., Chicago, May 2001. Structure, function, & inhibition of β-lactamase.

42. Dept. of Pharmacology, Vanderbilt Univ, Sept 2001. Structure, function & inhibition of β-lactamase

43. Procter & Gamble Pharma, Cincinnati OH, Oct 2001. Hits, leads, and artifacts from screening.

44. Chemical Biology Seminar Series, UCSF, Nov 2001. Stability & Functional Constraints on the Evolution of an Antibiotic Resistance Enzyme.

45. DOCK Users Meeting, San Francisco CA, Nov 2001. The Null Hypothesis.

46. Dept. of Chemical Engineering, Northwestern University, Nov 2001. The role of pre-organization in enzyme stability, activity, and evolution.

47. Syrrx, San Diego CA, Jan 2001. Docking vs. Screening vs. The Creature from the Black Lagoon.

48. Dept. of Chemistry, Michigan State University, Feb 2002. Hits, Leads, and Artifacts from Molecular Docking & Other Screens.

49. Boeringer-Ingelheim, Groton CT, Feb 2002. The Null Hypothesis in Molecular Docking.

50. UC Davis, Davis CA, 03/02. Structure, function, & inhibition of β-lactamase.

51. Johns Hopkins University, Dept. of Biophysics, Baltimore MD, 4/02. Stability & Functional Constraints on the Evolution of an Antibiotic Resistance Enzyme.

52. Abbott, Abbott Park IL, 4/02. Hits, leads, & artifacts from virtual & high throughput screening.

53. Dept. of Pharmaceutical Chemistry, University of California San Francisco, June 5 2002. Hits, Leads, and Artifacts from Virtual & High Throughput Screening.

54. GNF, San Diego CA, 07/02 Hits, Leads, and Artifacts from Virtual & High Throughput Screening.

55. SGX Inc, San Diego CA 07/02, Hits, Leads, & Artifacts from Virtual & High Throughput Screening.

56. Yale University Chemistry Dept, New Haven 09/02. Structure, function & inhibition of β-lactamase.

57. Bristol Myers Squibb, Princeton NJ 10/02. Hits, Leads & Artifacts from Screening. [email protected].

58. Blaffer Seminar Series, MD Anderson Cancer Center 01/03. Structure-based inhibitor discovery to combat antibiotic resistance.

59. University of Missouri, Kansas City MS 02/03. Hits, Leads & Artifacts from Docking & High Throughput Screening.

60. University of Chicago, 03/03. Hits, Leads, & Artifacts from Virtual & High Throughput Screening.

61. University of Washington, Seattle WA, 06/03. Structure, Function, & Inhibition of β-lactamase. ([email protected])

62. Pfizer Inc., Groton CT. 06/03. A mechanism for promiscuous inhibition and its occurrence among hits, leads, and drugs. Takushi Kaneko.

63. Wyeth Pharmaceuticals, Boston MA, 07/03. A specific mechanism for non-specific inhibition.

64. Chiron Inc., Alameda CA Aug 2003. Model systems for docking and database screening.

65. AstraZeneca Pharmaceuticals, Wilmington DE, Sept 2003. Model systems for docking and screening. [email protected]

66. University of Iowa, Iowa City Nov 2003. Model systems for molecular docking.

67. Univ of Michigan Dept. of Med. Chemistry, Ann Arbor MI, 11/03. Model systems for docking.

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68. Pfizer, Ann Arbor MI, November 2003. [email protected]. A mechanism for promiscuous inhibition and its occurrence among hits, leads, and drugs.

69. Neurocrine Pharmaceuticals, San Diego CA, November 2003. Model systems for molecular docking. [email protected]

70. Icos Pharmaceuticals, Seattle WA, Dec 3, 2003. A specific mechanism for non-specific inhibition.

71. Cornell Medical School, New York City, Feb 2004. Model systems for molecular docking.

72. AstraZeneca Pharmaceuticals, Boston MA, Feb 2004. Docking vs. Screening vs. The Creature from the Black Lagoon. [email protected]

73. Pharmacopeia, Cranbury NJ, April 2004. A specific mechanism for non-specific inhibition. [email protected].

74. University of North Carolina, Chapel Hill, April 2004. Model systems for molecular docking.

75. Univ. Wisconsin Madison WI. May 2004. A specific mechanism for non-specific inhibition.

76 Genelabs, South San Francisco CA, June 2004. Model systems for molecular docking.

77. Plexxicon. Berkeley CA. May, 2004. Model systems for molecular docking.

78. Telik. S. San Francisco June 2004. Hits, leads & artifacts from virtual & high-throughput screening.

79. Pfizer. St. Louis MO. July 2004. A mechanism for promiscuous inhibition and its occurrence among hits, leads, and drugs.

80. Mobashery Symposium, Notre Dame University, Indiana. Oct 2004. Structure, function, & Inhibition of β-lactamases.

81. Stanford Univeristy Dept. of Molecular Pharmacology, Palo Alto CA. Oct 2004. Model systems for molecular docking. (student Relly Brandon)

82. Case Western Reserve University, Cleveland OH. Nov 2004. Structure, function, & inhibition of β-lactamases. ([email protected])

83. Univ Arizona Dept. Med. Chem., Arizona, Jan 2005. A mechanism for promiscuous inhibition and its occurrence among hits, leads, and drugs.

84. University of Pittsburgh, Center for Computational Biology & Bioinformatics. Model systems for molecular docking. Feb 2005

85. Dow Agrochemicals, Indianopolis IN. Model systems for molecular docking. March 2005. Dan Pernich [email protected]

86. University of Pennsylvania, Philadelphia PA. Model systems for molecular docking. May 2005

87. Vitae Pharmaceuticals, Philadelphia PA. Model systems for molecular docking. May 2005 Guosheng Wu ([email protected])

88. Theravance, South San Francisco CA. Docking & Its Discontents. June 9 2005. Ed Moran.

89. Achaogen, South San Francisco CA. A specific mechanism for non-specific inhibition. June 2005.

90. Scios, S. San Francisco. Docking vs screening vs the creature from the Black Lagoon. July 2005.

91. Institute for Diabetes Discovery, Bradford CT. A specific mechanism for non-specific inhibition. Aug 2005. [email protected]

92. CARB, Baltimore MD. Model systems for virtual screening. Sept 2005. Mike Gilson.

93. University of Southern California, Los Angeles. Model systems for docking. Nov 2005.

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94. Johns Hopkins University, Dept. of Biophysics and Biochemistry. Inhibition & Molecular Evolution of β-lactamase. Feb 2006. John Lorsch, [email protected]

95. Burnham Institute, San Diego CA. Structure-based screening & chemical information. June 2006. Host: Robert Liddington.

96. Eli Lilly, Indianapolis IN. Predicting Protein Activities Using Structure & Chemical Information. July 2006. [email protected]

97. Roche Pharma., Palo Alto CA. Chemical and Target Complexity in Virtual Screening. Sept 25, 2006. [email protected]; [email protected]

98. Novartis: “Novartis Chemistry Lectureship”, Cambridge MA. Hits, Leads, and Artifacts from High-Throughput and Virtual Screening. Oct 2006. [email protected]

98. Wyeth Pharmaceuticals, Cambridge MA. Models systems for docking. Oct 2006. diane mccarthy.

99. Arizona State University, Tempe AZ. Model systems for docking. Nov 2006. [email protected]

100. UC Berkeley, Chemistry/Mol. Biology Seminar series. Berkeley CA. Sept 2006. Docking vs. screening vs. the creature from the black lagoon. Tom Alber.

101. University of California, Santa Barbara. Jan 2007. Given an enzyme, what does it do? Given a drug, what are its targets? [email protected]

102. Virginia Commonwealth University, Richmond VA 23298. Feb 2007. Predicting Protein Activities Using Structure & Chemical Information. [email protected] (susanna wu)

103. Medicinal Chemistry Dept., University of Minnesota, Minneapolis MN. April 2007. Yusuf Abul-Hajj, [email protected]

104. Dept. of Pharmacology, UNC, Chapel Hill. May 15, 2007. Relating protein pharmacology by ligand chemistry. Bryan Roth.

105. Wyeth Pharmaceuticals, Boston MA. May 16, 2007. New methods in molecular docking.

106. Dept. of Medicinal Chemistry, Purdue West Lafayette. April 24, 2008. New ligands for old targets and new targets for old drugs. Chiwook Park, [email protected]

107. Dept. of Chemistry, UC Riverside. May 2, 2008. [email protected].

108. Merck Research Labs, Rahway NJ. Aug 15, 2008. [email protected]. A specific mechanism for non-specific inhibition.

109. Dept. of Chemistry, UC Davis. Nov 6, 2008. [email protected]. Why does high-throughput screening ever work?

110. Frontiers in Biology Seminar Series, Stanford University Palo Alto CA. Dec. 10, 2008. A Chemical View of Pharmacological Networks.

111. Experimental Therapeutics Group, MD Anderson Cancer Center. Jan 14, 2008. [email protected]. Predicting new ligands for G-Protein Coupled Receptors.

112. Chemistry Dept. UC Santa Cruz. Jan, 2009. Screening for novel inhibitors: why should it ever work?

113. OSI Pharmaceuticals, Long Island NY. March 24, 2009. Docking vs. Screening vs. the Existential Emptiness of Chemical Space.

114. Abbott Lectureship, Yale University. March 25, 2009. [email protected]. New ligands for old targets and new targets for old drugs.

115. Broad Institute, MIT Cambridge MA. May 2009. Forward & reverse chemical information in biology.

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116. Case Western Dept. of Pharmacology, Cleveland OH. Oct 19-20 2009. New ligands for old targets and new targets for old drugs. Krysztof Palzeski/[email protected]

117. Ohio State University, Columbus OH. Oct 21 2009. New ligands for old targets and new targets for old drugs. Chenglong Li/[email protected]

118. Institute for Genomics and Bioinformatics Distinguished Speaker Series, UC Irvine. March, 2010. New ligands for old targets and new targets for old drugs. Katarina Fletcher/Pierre F. Baldi, Professor, Director, [email protected].

119. Vanderbilt University, Dept. of Biochemistry, Nashville TN. March 2010. New ligands for old targets and new targets for old drugs. Jens Meiler.

120. Pfizer, Groton CT. March 2010. Colloidal Aggregation and its Role in Screening and Drug Behavior.

121. Pfizer, Groton CT. March 2010. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space.

122. Stanford University, Stanford CA. Symbios Seminar Series. March 2010. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space.

123. Novartis, Emoryville CA. New ligands for old targets and new targets for old drugs.

124. AstraZeneca, Boston MA. July, 2010. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space.

125. Merck Research Labs, Westpoint PA. Oct 2010. New ligands for old targets and new targets for old drugs. [email protected]

126. Washington University Biochemistry Lecture Series, St. Louis MO. The chemical basis of pharmacology. Jan 2011. [email protected]; [email protected]

127. Vertex Pharmaceuticals, Boston. New ligands for old targets and new targets for old drugs. May, 2011.

128. NYU Frontiers in Pharmacology, New York City. May 10, 2011. New ligands for old targets and new targets for old drugs. [email protected].

129. UCSD Pharmacology Seminar Series, San Diego. May 17, 2011. New ligands for old targets and new targets for old drugs. Taylor Gilliland [email protected]

130. Topliss Lectureship, Univ. of Michigan Dept. of Medicinal Chemistry, Ann Arbor MI. Sept 22-23, 2011. The Chemical Basis of Pharmacology. Scott Larson [email protected]

131. Hauptmann-Woodward Institute, Buffalo NY. Oct 6, 2011. Docking vs. Screening vs. the Gobsmacking Emptiness of Chemical Space. Tim Umland [email protected]

132. Univ. of Wisconsin Dept. of Pharmacology, Madison WI. Nov 1 2011. The Chemical Basis of Pharmacology.

133. Harvard Medical School, Dept. of Systems Biology, Boston MA. Nov 7 2011. The Chemical Basis of Pharmacology.

134. Novartis Pharma, Emeryville CA. Docking vs. screening vs. β-lactamase. Jan 2012.

135. University of South Florida, Tampa Florida. Feb 17 2012. Docking, screening and the gobsmacking emptiness of chemical space. Yu Chen.

136. Vertex Pharmaceuticals, San Diego CA. March 2012. Structure-based discovery vs. GPCRs.

137. St. Judes Research Institute, Memphis TN. April, 2012. The chemical basis of pharmacology. Richard Lee.

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138. Achaogen Pharma, South San Francisco CA. April 2012. Docking vs. sceeening vs. β-lactamase.

139. University of Texas, Austin. Department of Medicinal Chemistry. May 24, 2012. Docking, screening and the gobsmacking emptiness of chemical space. Kevin Dalby.

140. Memorial Sloan-Kettering Cancer Center. New York City, NY. Docking, screening and the gobsmacking emptiness of chemical space. Derek Tan. June 12, 2012.

141. Genentech. South San Francisco, CA. Backward and Forward with Molecular & Classical Pharmacology. Sept, 2012. Jeff Blaney.

141. Mount Sinai School of Medicine, Dept. of Chemical and Structural Biology. New York City, NY. The Chemical Basis of Pharmacology. Oct 25, 2012. Roberto Sanchez.

142. Johns Hopkins University Dept. of Pharmacology. Baltimore, MD. The Chemical Basis of Pharmacology. Oct 2012.

143. J&J Pharmaceuticals. San Diego, CA. The Chemical Basis of Pharmacology. Jan 2012.

144. Medical College of Wisconsin, Dept. of Biochemistry, Milwaukee WI. Backward and Forward with Molecular and Classical Pharmacology. Sept 11, 2013.

145. Morgridge Institute, Presentation to SAB on “The role of computation in chemical biology”, Sept 24, 2013, Brad Schwartz, [email protected]

146. University of Indiana Dept. of Biochemistry, Bloomington IN, The Metabolic Code. Erin Carlson. Oct 3-5, 2013.

147. Distinguished Scientist Seminar, University of Pittsburgh. Pittsburgh PA. The Metabolic Code. Nov 18, 2013 (Ivet Bihar).

148. Cold Spring Harbor Lab, Long Island NY. Target-based discovery, ligand-based discovery, and the metabolic code. Leemor Joshua-Tor. Nov 14, 2013.

149. University of Toronto, Dept. of Chemistry. Backward and Forward with Molecular and Classical Pharmacology. Nov 22, 2013.

150. Universite de Sherbrooke, Dept. of Chemistry. Backward and Forward with Molecular and Classic Pharmacology. Dec, 2013.

151. University of Ottawa, Ottawa Ontario. The Metabolic Code and the Origins of Cell Signaling. Jan 30, 2014.

152. Dept of Chemistry, Brandeis University, Boston MA. The Metabolic Code. April, 2014. [email protected].

153. University of Rochester, Rochester NY. Backward & Forward with Molecular & Classical Pharmacology. May, 2014.

154. School of Pharmacy, Distinguished Lecturer, The Ohio State University, Columbus Ohio. Backward & Forward with Molecular & Classical Pharmacology. Nov 2014. Henry Mann.

155. Arthur Broom Lecture, University of Utah School of Pharmacy. March 16, 2014, Salt Lake City, Utah. Shawn Owen. A metabolic code for cell signaling

156. McGill University Dept of Biochemistry, Montreal PQ. A metabolic code for cell signaling. May 2015

157. Bernard Belleau Lecture, McGill University Dept of Chemistry, Montreal PQ. Empirical and virtual screening for ligand discovery and receptor deorphanization. May 12, 2015.

158. Virginia Tech University, Dept of Chemistry, Blacksburg VA. Structure-based Probe Discovery for GPCRs. Sept 18, 2015. Felicia Etzkorn.

159. UNC Drug Discovery Symposium, Chapel Hill NC. A metabolic code for cell signaling. Oct 15 2015. Bryan Roth.

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160. Dept. of Biochemistry, University of Chicago, Chicago IL. A Cure for Pain: Structure-based Probe Discovery for GPCRs. Oct 28, 2015. Demet Arac-Ozkan [email protected] (faculty) Julian Owens [email protected] (admin).

161. Dept. of Chemistry, UCLA, Los Angeles CA. Docking for new chemotypes with new pharmacology for GPCRs. Ken Houk. April 26, 2016.

162. Dept. of Chemistry, Boston College, Boston MA. May 10, 2016. Docking for new chemotypes with new pharmacology for GPCRs.

163. Pfizer Inc. Cambridge MA. May 11, 2016. New chemotypes illuminate new biology for orphan and opioid GPCRs. Mark Bunnage.

164. Dept of Biochemistry & Molecular Pharmacology, Harvard University Medical School, Boston MA. May 12, 2015. Docking for new chemotypes with new pharmacology for GPCRs. Andy Kruse.

165. Memorial Sloan-Kettering Cancer Center. New York City, NY. A metabolic code for cell signaling (or, A cure for pain). John Chodera. June 16, 2016.

166. University of Illinois Chicago. Chicago, IL. The Roles of Colloidal Aggregation Throughout Compound Progression. Sept 16, 2016. Guido Pauli, [email protected].

167. Universite de Montreal. Montreal, Quebec. Novel GPCR ligands with novel biology. Nov 7, 2016. [email protected]

Service Federal Government Service 2001 Ad hoc member of NIH IRGs: BBCA, SSS-B, NIDA-Medication Development 2002-2003 Ad Hoc Member of NIH IRG SSS-L 2003 Ad hoc member of NIH IRG BBCA, SSS-H 2003-2004 Member of NIH BDMA 2004-2009 SAB, NIH RoadMap Chemical Libraries and Screening Initiative 2005-2008 Chartered Member of NIH SBC-B 2005 Chairman, NIH ZRG1 BCMB-G91S Study Section 2008-2010 Chairman, NIH HTS Study Section ZRG1 BST-J. 2014-present Chartered Member of NIH Study Section MSFA

University & Public Service Committee Service (Northwestern University) University Committees 1997-1998 Keck Biophysics Facility Organization and Purchasing Committee (J. Widom) 1997-present MSTP admissions committee 1998-present Keck Biophysics Facility Steering Committee 1999-present NIH Biophysics Training Grant (T32) Steering Committee 1999 NU Computation Strategy Committee 2000 Bioinformatics Strategy Committee (organized by the VP for Research)

Medical School Committees 1997-2000 Library Committee 1998 IGP Admissions committee 1999-2000 IGP recruitment handbook committee

Faculty Search Committees 1996-1997 MPBC Search Committee: Doug Freymann recruited.

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2000-present MPBC/Ovarian Search Committee. 2001-2002 NUIN/MPBC Faculty Search

Departmental Committees 1996 Departmental executive committee 1998-2002 Departmental executive committee 1996-2002 Seminars committee 1996-2001 Drug Discovery Program education committee 1999-2000 VIACORE Dept. vision committee reporting to the provost

Committee Service (UCSF) University of California Wide Committees 2008—2010 GREAT Program Review Committee University Committees 2003-2010 Biophysics Admissions committee 2003-2008 Biophysics Executive committee 2003-2009 CCB Admissions Committee 2004-2008 Chair, CCB Admissions committee 2004-2006 UCSF Rules Committee 2003 Asilomar Organizer 2005 Asilomar Retreat Committee (BMI Rep) 2005-2009 RAB Committee 2005-2013 Conflicts of Interest Committee 2005-2009 SMDC Executive Committee 2005 Dean’s Pew Scholar’s Committee 2008—2013 BSRROC Sandler Committee 2008—2012 Mission Bay Lecture Committee 2011—2013 Biophysics Admissions committee 2015 Keck Fellowships Pre-Review Committee 2015-present Biophysics Admissions committee School of Pharmacy Committees 2004-2009 Dean’s Strategic Planning Committee 2005-2007 Dean’s Infrastructure Committee 2005-2009 SOP Awards Committee 2008 Pharmacy Admissions Interviewer 2008-2009 Pharmacy Admissions Committee 2014-present SoP Faculty Council 2014-present Pharmaceutical Sciences Pathway Committee 2016-present Curriculum Revision Committee

Faculty Search Committees 2003 BMI Faculty Search UCSF 2004 BMI Faculty Search UCSF 2004-2005 CMP/QB3 Search committee 2005-2007 Pharm. Chem/CMP Search committee

Departmental Committees 2007—08; 2011-12 Vice Chair, Dept. of Pharmaceutical Chemistry Teaching & Mentoring Graduate Education & Courses 1996-present Ph.D. Research Mentor, a total of 18 students

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Northwestern University 1996 IGP Core course in Biochemistry (6 hours, ~30 students) 1997-1998 Dental Pharmacology (3 hours, ~40 students) 1997 Advanced Dental Pharmacology (6 hours, ~10 students) 1997-present IGP Core course in Biochemistry (4 hours, ~30 students) 1997-1999 Modern Topics in Drug Discovery (3 hours, 6 to 8 students) 1998-present Molecular Bases of Drug Action (4 hours, ~25 students) 1998-1999 Biotech Program Course in Bioinformatics (3 hours, ~20 students) 1997-present Macromolecular Structure & Function (8 hours, ~4 students) 2001 Lectures in Life Sciences Journal Club (1 hour, ~28 students) 1999-present Macromolecular Structure & Function Journal Club (12 hours, 10 students) 1998-1999 Independent Study, WCAS 1 student Medical Education & Courses (Northwestern Univ) 1996-1999 Scientific Basis of Medicine (4 hours, ~180 students) 2000-2002 Scientific Basis of Medicine (6 hours, ~180 students) 2000 Small Group Session on Genetic disorders (2 hours, 30 students) 1999-2002 MSTP Journal Club (3 to 8 hours, 6 to 10 students) 1996-2002 Medical School Summer Research (1 medical student/summer) 2001 Biomedical Sciences for Physician Research Fellows (1.5 hours, 10 M.D.s)

Teaching Administration (Northwestern Univ) 1997 Chairman’s committee to design the new graduate pharmacology course. UCSF Graduate Courses 2004-2006 Computational Biophysics (5 hours, Spring Quarter ~8 students) 2007-2010 BMI206 (6 hours, Spring Quarter ~20 students) 2004, 2007-2010 PSPG 220 (10 hours, ~20 students) 2006-present BBC Journal Club Procter, 45 hrs, 60 students 2006 “Pharmacy 101”, 3 hrs, 20 non-UCSF community members (UCSF-sponsored)

Pharmacy Courses 2004-2013 PC152 Drug Discovery (30 hours, Spring Q, 8-20 students) 2009-2013 PC111 Physical Chemistry (6 hours, Fall Q, 122 students) 2015- present PC111 Physical Chemistry (2 hours, Fall Q, 122 students)

Trainees Graduate Student Trainees 1996-1997 Donatella Tondi, Ph.D. Dottore University of Modena.

Present position: Assoc. Professor, University of Modena .

1996-2001 David Lorber Ph.D, B.A. Illinois State University. Present position: Senior Scientist, Accelrys Inc.

1997-2002 Rachel Powers Ph.D., B.A. Michigan State University, IGP graduate student. Present Position: Assoc.. Prof, Grand Valley State University, Michigan.

1998-2002 Beth Beadle Ph.D., B.A. Northwestern University, MSTP graduate student. Present: Asst. Professor, MD Anderson Cancer Center

1998-1999 Emilia Caselli, Ph.D. Dottore University of Modena. Ph.D. Present: Staff Scients, University of Modena.

1999-2003 Binqing Wei Ph.D, B.A. Nanjing University. Present: Scientist, Genentech..

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1999-2003 Susan McGovern Ph.D., B.A. Notre Dame University, MSTP graduate student. Present: Physician-Scientist,. MD Anderson Cancer Center

2003-2005 Federica Morandi, Dott. Present position: Scientist, Merck-Serano, Bilerica, MA.

2002-2007 Alan Graves, B.A. Vanderbilt University. Biophysics Graduate student Present position: Scientist, Glaxo Smith Kline, Philadelphia PA

2003-2007 Brian Feng, B.A. UT Austin. CCB Graduate student Present position: Scientist, Novartis Emeryville CA.

2004-2008 Kristin Coan, B.Sc. Reed College, Portland CCB Graduate student Present position: Scientific writer, Basel, CH.

2003-2009 Veena Thomas, B.Sc. MIT Cambridge. PSPG Graduate student Present Position: Postdoc Stanford Univ. with Vijay Pande

2004-2009 Sarah Boyce, B.Sc. CCB Graduate student Present Position: Scientist, Schroedinger Pharma

2005-2009 Mike Keiser, B.Sc. Stanford Univ, CA BMI Graduate student Present Position: Asst. Professor, UCSF

2006-2010 Rafaela Ferreira, B.Sc. CCB Graduate Student Present Position: Assistant Professor, Brazil

2006-2012 Michael Mysinger, MSc. Stanford Univ, PSPG Graduate student Present Position: Scientist, ConfometRx

2008-2013 Gabriel Rocklin, B.Sc. UCLA Biophysics Graduate Student Present Position: Postdoc, David Baker Lab

2009-2014 Henry Lin, B.Sc. UC Berkeley BMI Graduate student Present Position: Scientist, J&J Pharma

2010-2014 Joel Karpiak, Johns Hopkins University CCB Graduate student Present Position: Scientist, GlaxoSmithKline Postdoctoral Fellows 1996-1998 Scott Weston, Ph.D. University of Mississippi

Asst. Prof. University Incarnate Word, Feik School of Pharmacy, San Antonio TX

1999-2002 Xiaojun Wang, Ph.D. Chicago Medical School Present Position: Senior Scientist, Abbott Pharmaceuticals

2000-2003 George Minasov, Ph.D., Tbilisi State University Present Position: Research Associate, Northwestern University

2002-2003 Jim Horn, Ph.D., University of Iowa Present Position: Assistant Professor, Northern Illinois University

2003-2005 Ruth Brenk, Ph.D, Marburg University Germany Present Position: Assistant Professor, University of Dundee, Scotland

2003-2007 Niu Huang, Ph.D, University of Maryland Present Position: Asst. Professor, Nat. Inst. of Bio. Sciences, Beijing China

2004-2007 Johannes Hermann, Ph.D, University of Dusseldorf Present Position: Scientist, Roche Pharmaceuticals, Palo Alto CA.

2005-2007 Kerim Babaoglu, Ph.D, University of Tennessee/St. Judes Medical Center Present Position: Scientist, Gilead Pharmaceuticals, Foster City CA.

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2006-2008 Jerome Hert, Ph.D, Sheffield University, UK Present Position: Research Scientist, Roche Pharmaceuticals

2003-2009 Yu Chen, Ph.D, University of Chicago Present Position: Asst. Professor, Univ. of South Florida

2007-2009 Denise Teotico, Ph.D., University of North Carolina Chapel Hill Present Position: Research Scientist, GlaxoSmithKline, RTP

2009-2010 Kong Nguyen, Ph.D., University of Berne, Switzerland Present Position: Postdoc with Matthieu Schapira, SGC Toronto.

2007-2011 Peter Kolb, Ph.D., University of Zurich, Switzerland Present Position: Asst. Professor, Univ. of Marburg

2009-2011 Jens Carlsson, Ph.D. Uppsala University, Sweden Present Position: Asst. Professor, Uppsala Univ, Sweden

2010-2011 Kristin Ziebart, Ph.D. Univ. of California Davis Present Position: Lecturer, UC-Davis

2008-2012 Christian Laggner, Ph.D., University of Innsbruck, Austria Present Position: Staff Scientist

2008-2013 Oliv Eidam, Ph.D., University of Zurich, Switzerland Present Position: Scientist, Roche Pharma, Basel Switzerland

2009-2012 Elisabet Gregori, Ph.D., Univ. of Barcelona, Spain Present Position: Scientist, Novartis Cambridge USA

2009-2013 Dahlia Weiss, Ph.D., Stanford University Present Position: Scientist, Heptares Pharma, UK

2007-2013 Matt Merski, Ph.D., Johns Hopkins University Present Position: Staff Scientist, Poland

2009-2014 Ryan Coleman, Univ. of Pennsylvania Present Position: Scientist, Sandia Natl. Labs

2010-present Magdalena Kryznska, McGill University, Canada 2011-present Sarah Baralier, Univ. de Montpellier, France Present Position: New Mom, looking for a job in France. 2011-present Marcus Fischer, Univ. Of York, United Kingdom 2012-present Trent Balius, SUNY Stony Brook 2013-present Matt O’Meara, UNC Chapel Hill 2013-present Da Duan, Queens University, Kingston Ontario Canada 2013-present Anat Levit, Hebrew University, Jerusalem Israel 2016-present Josh Pottel, McGill University, Montreal QC, Canada. Senior Scientists 1997-2000 Alexandera Patera, Ph.D. Brandeis University Present position: Northwestern University IBiS Grad. Program Administrator.

2000-present John Irwin, Ph.D. ETH Zurich. Medical Student Trainees 2000-2002 Indi Trehan, B.A. University of California, Medical Student Research Fellow. HHMI

Medical Student Research Fellowship, $58,0000.

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2002-2003 Tomer Roth, B.A. University of California, Medical Student Research Fellow. HHMI Medical Student Research Fellow, $32,000.

Visiting & Sabbatical Scholars (17) 9/1/98 to 9/30/98 Professor Jesus Blazquez Hospital Ramon y Cajal, Madrid Spain (Sabbatical) 8/17/98 to 8/31/98 Angela Lee, Ph.D. National Cancer Institute, Frederick MD 9/1/98 to present Professor Maria Udo Loyola University, Chicago (Sabbatical) 8/15/99 to 8/17/99 Lakshmi Kotra, Ph.D Wayne State University (Prof. Shahriar Mobashery) 1/19/00 to 1/20/00 Robert Bonomo, M.D. Cleveland VA Hospital 4/1/00 to 4/15/00 Laurie Jackson (grad stud.) UT Southwestern (lab of Prof. Meg Phillips) 07/15/00 to 07/31/00 Toni Dow (grad student) Yale University (lab of Prof. Karen Anderson) 2/15/01 to 3/1/2001 Yue Pan (grad student) Northwestern Univ., Dept. of Chemistry 03/01/01 to 4/31/01 Dr. Anna Vulpetti Pharmacia Inc, Nerviano Italy 02/15/01 to 03/01/01 Darrell Hurt (grad student) Cornell University (lab of Prof. John Clardy) 04/02/01 to 04/05/01 Dr. Douglas Rohrer Pharmacia Inc, Kalamazoo MI 04/16/01 to 04/30/01 Dr. Leo Grinius Procter & Gamble, Cincinnati OH 01/20/03 to 01/31/03 Dr. Beth Collantes Pharmacia Inc, St. Louis MO 01/03/03 to 04/30/03 Prof. Ken Olsen Loyola University, Chicago IL (Sabbatical) 10/01/03 to 09/30/04 Prof. Richard Bonnet Universite de Clairmont, France (Sabbatical) 03/2005 to 06/2005 Prof. Cynthia Selassie Pomono College (Sabbatical) 07/2005 to 10/2005 Prof. Gerhard Klebe Marburg University, Germany (Sabbatical) 01/2007 to 06/2007 Prof. Enoch Baldwin University of California, Davis (Sabbatical) 07/2007 to 08/2007 Prof. Olaf Wiest Notre Dame University (Sabbatical) 08/2015 to 12/2015 Prof. Gary Rudnick Yale University (Sabbatical) Graduate Student Research Rotations (Northwestern University) 1996 David Lorber (NUIN) 1997 Rachel Powers (IGP) 1998 E.J. Dell (IGP); Binqing Wei (NUIN); Susan McGovern (MSTP) 1999 Huang Shen (IGP) 2000 Xin He (IGP); Ursula Ramirez (NUIN); Allison Rufatto (NUIN) 2001 Holly Hanford (IGP); Austin Kirschner (MSTP); Alan Graves (IBiS) 2002 Jia Lee (NUIN); Scott Brattle (IGP); Brian Feng (IGP/CCB)

Graduate Student Research Rotations (UCSF) 2003 Ray Nagatani (PSPG) 2003 Veena Thomas (PSPG) 2003 (fall) Arjun Narayanan (Biophysics); Janet Chung (CCB); Baran (PSPG) 2004 (winter) Morri Feldman, Greg Friedland (both Biophysics), David Smithson (CCB) 2004 (spring) Sarah Boyce (CCB), Holly Atkinson (BMS), Abram Calderon (CCB) 2004 (summer) Kristin Coan (CCB) 2004 (fall) Grant Shackleford (CCB) 2005 (winter) Elisabeth Humphris (BP), Mike Keiser (BMI) 2005 (spring) Kareen Rivers (PSPG)

Undergraduate Research Trainees 1997-1998 Andrew Su, WCAS ISP (now a group leader at Genomics Inst. of Novartis). 2003 David Minh, UC Berkeley

Thesis Committees (Northwestern University) 1996 Maxwell Cummings (Rand Read, PI), external member, University of Alberta 1999-present E.J. Dell (H. Hamm’s lab) 2000-2002 Elena Brin (J. Leis’s lab) 2000-2002 Hena Alam (D. Freymann’s lab)

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2001-2003 Ursula Ramirez (D. Freymann’s lab) 1998-2000 Gregory Harbers (Kevin Healey’s lab) 2001-2003 James Patch (Annelise Barron’s lab) 2002-2002 Greg Snyder (Sue Pierce’s lab)

Thesis/Orals Committees (UCSF) 2003 Alex Schnoes (Cohen lab) 2003 Ben Polaco (Babbitt lab) 2004 Byoung-Chul Lee (Dill lab, Committee Chair) 2004 Alex Schnoes (Babbitt lab) 2004 Ray Nagatani (Babbitt lab, Committee Chair) 2004 Fred Davis (Sali lab, Committee Chair) 2005-2009 David Smithson (Guy lab) Summary of Teaching Hours 2003-2004 About 430 hours

Formal classroom teaching 40 hours. Prep time 180 hours (all new lectures). Mentoring Students 200 hours. Mentoring Junior Faculty 10 hours.

2004-2005 About 430 hours Formal classroom teaching 45 hours. Prep time 120 hours (some new lectures). Mentoring Students 250 hours.(lab growing) Mentoring Junior Faculty 15 hours.

2005-2006 About 400 hours Formal classroom teaching 40 hours. Prep time 100 hours (some new lectures). Mentoring Students 250 hours.(lab stable) Mentoring Junior Faculty 15 hours.

2006-2013 About 400 hours Formal classroom teaching 40 hours. Prep time 100 hours (some new lectures). Mentoring Students 250 hours.(lab stable) Mentoring Junior Faculty 10 hours.

2014-present About ~275 hours Formal classroom teaching ~6 hours (PC111, other PharmD and medical resident teaching). Prep time 30 hours (some new lectures). Proctoring iPQB Journal club (45 hrs in class time) Mentoring Students 200 hours

I estimate formally mentoring of students and postdocs in my lab based on my regular, individual weekly meetings with them, excluding group meetings. Teaching Narrative At UCSF I taught PC152, which functions as an introduction to modern methods in drug discovery as well as a course preparing for formal research. The focus was on both didactic training but also on discussion sections, formal presentations, grant writing and researching areas of research for themselves. The course is designed for research track PharmDs, but about an equal number of graduate students and postdocs also take it. Between 16 to 20 students took the course yearly. Team-taught courses to which I contributed include BMI206, a biophysics/computational biology graduate course, and PC111, physical chemistry for pharmacists. The former focuses on modern

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methods in molecular docking and virtual screening, the latter on classical physical chemistry and, in my six lectures, on its role in drug discovery. About 30 graduate students took BMI206 and 122 PharmDs take PC111.

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microsoft...brian shoichet, cv august, 2016 university of california brian shoichet, curriculum...

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