c3c3 introduction into ci; ss 03/1st lecture © gasteiger et al. chemoinformatics in europe:...
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![Page 1: C3C3 Introduction into CI; SS 03/1st lecture © Gasteiger et al. Chemoinformatics in Europe: Achievements and Perspectives Johann Gasteiger Computer-Chemie-Centrum](https://reader035.vdocuments.us/reader035/viewer/2022070414/5697c0241a28abf838cd4d53/html5/thumbnails/1.jpg)
C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Chemoinformatics in Europe:Achievements and Perspectives
Johann GasteigerComputer-Chemie-Centrum
University of Erlangen-Nürnberg
D-91052 Erlangen, Germany
www2.chemie.uni-erlangen.de/
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Overview
• chemoinformatics - definition
• the bright past
• the grim presence
• the bright future ?
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Synthesis of Properties
The most fundamental and lasting objective of synthesis is not
production of new compounds
but
production of properties
George S. HammondNorris Award Lecture, 1968
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
What structure do I need for a certain property?structure-activity relationships
How do I make this structure?synthesis design
What is the product of my reaction?reaction predictionstructure elucidation
Fundamental Questions in Chemistry
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Chemoinformatics - Why?
• complex relationships
structure - biological activity
chemical reactivity
• amount of information
many millions of compounds and reactions
many millions of publications
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
From Data to Knowledge
know-ledge
information
data
generalization
context
measurementcalculation
deductivelearning
inductivelearning
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Chemoinformatics: Definition
The application of
informatics methods
to solve
chemical problems
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Application Areas for Chemoinformatics
• drug design
• analytical chemistry
• chemical engineering
• inorganic chemistry
• medicinal chemistry
• organic chemistry
• physical chemistry
• theoretical chemistry
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
chemicalstructure
physicalproperty
chemicalproperty biological
property
starting materials
synthesisplanning
reactionpredictionstructure
elucidation
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
The Scope of Chemoinformatrics
• structure representation and searching
• data analysis and chemometrics
• molecular modeling
• spectra analysis and structure elucidation
• reaction representation and searching
• reaction modeling and synthesis design
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
• structure representation
1965, Morgan• structure elucidation
1965, Sasaki, Munk, DENDRAL• synthesis design
1970, Corey & Wipke, Ugi, Gelernter, Hendrickson• molecular modeling
1970, Langridge, Marshall• data analysis / chemometrics
1970, Kowalski, Wold
Chemoinformatics – An Old Discipline
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
• data storage and retrieval
• property prediction
• drug design
• synthesis design
• spectra analysis and prediction
Common Topics: Structure Representation
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Common Topics: Data Analysis Methods
• property prediction
• drug design
• analytical chemistry
• spectra analysis and prediction
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
gene drugprotein lead
Bioinformatics Chemoinformatics
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Biochemical Pathways
/slides/Biochemical_Pathways/Folien/CCC/roche_2.ppt© Gasteiger et al.C3
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al. /slides/Biochemical_Pathways/Folien/CCC/gcb00.ppt© Gasteiger et al.C3
What is a Chemical Reaction?
+
the bioinformaticianan event influenced by a gene, a protein
the computer scientista context sensitive graph rewriting rule
the chemistan event breaking and making bonds
EC - Nr.: 4.1.3.7COOH
C
CH2
O
COOH
CH3 CO
S CoA
COOH
CH2
C
CH2
COOHHO
COOH
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Glucose6-phosphate
NADP+
NADPH H+
6-Phospho-gluconolactone
H2O
6-Phospho-gluconate
Ribulose5-phosphate
CO2
Xylulose5-phosphate
Ribose5-phosphate
Glyceraldehyde3-phosphate
Sedoheptulose7-phosphate
Erythrose4-phosphate
Fructose6-phosphate
H+NADP+NADPH
1
3
45
6
2
5
9
24
7
8
10 11
14
Glyceraldehyde3-phosphate
15
1
23
45
67
8
10
12
12 13
14
1512
5[r10] 5[r12] 10[r14] 10[r1] 10[r2] 10[r3] 8[r4] 3[r6] 3[r8]
2[c13] 20[c2] 10[c6] 1[c8] ---> 20[c4] 20[c5] 10[c9] 3[c12]
maximize NADPH production
Pathway Searching
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Handbook of Chemoinformatics
J. Gasteiger (Editor)
65 authors73 contributions
4 volumes1900 pages
Wiley-VCH, Weinheim(August 2003)
From Data to Knowledge
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Textbooks on Chemoinformatics
• V. Gillet, A. Leach
• J. Gasteiger, T. Engel
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Major Contributions from Europe
• structure representation• data analysis methods• databases• research centers• funding• industry• teaching
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Structure Representation (Europe)
European industry: BASF, Hoechst, ICI, Thomae,
BASIC, IDC
Sheffield: M. Lynch, P. Willett
Munich: I. Ugi, J. Gasteiger, C. Jochum
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Data Analysis Methods (Europe)
PLS: S. Wold
Self-organizing neural network: Kohonen
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Databases (Europe)
Cambridge CSD
Inorganic Structures Database
Beilstein
Gmelin
ChemInformRX
SpecInfo
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Institutions and Research Centers (Europe)
FIZ Karlsruhe, D
FIZ Chemie, D
CAOS/CAMM Center, Nijmegen, NL
Computer-Chemie-Centrum, Erlangen, D
Center for Molecular Informatics, Cambridge, UK
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Funding (Germany)
Fachinformationsprogramm 1981 - 1994
German Federal Minister of Research and Technology (BMFT)
(Dr. Riesenhuber, chemist !)
institutions
FIZ Karlsruhe
FIZ Chemie
databases
Beilstein
Gmelin
ChemInformRX
SpecInfo
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Industry (Europe)
• early work on databases
• positions in chemoinformatics
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Teaching (Europe)
Sheffield
UMIST
Strasbourg
Erlangen
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Databases (Europe)
Cambridge CSD
Inorganic Structures Database
Beilstein -
Gmelin -
ChemInformRX -
SpecInfo
however:
distributed by
MDL Elsevier
expensive;
academia cut off?
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Institutions and Research Centers (Europe)
FIZ Karlsruhe, D
FIZ Chemie, D
CAOS/CAMM Center, Nijmegen, NL
Computer-Chemie-Centrum, Erlangen, D
Center for Molecular Informatics, Cambridge, UK
however:no research
no research
no long-term commitment
successor to J. Gasteiger ?
no long-term commitment
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Funding (Germany)
Fachinformationsprogramm 1981 - 1994
German Federal Minister of Research and Technology (BMFT)
(Dr. Riesenhuber, chemist !)
institutions
FIZ Karlsruhe
FIZ Chemie
databases
Beilstein
Gmelin
ChemInformRX
SpecInfo
however:
now all BMBF projects
go into
bioinformatics
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Industry
• early work on databases
• positions in chemoinformatics
however:• hardly any in-house
work done anymore• mergers lead to
elimination of positions
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Teaching (Europe)
Sheffield
UMIST
Strasbourg
Erlangen
however:
discontinued?
only for Molecular Science students
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Funding (Europe)
6th Framework program of the European Union:
several programs for Bioinformatics
however: no mention of Chemoinformatics!
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
What Can be Done?
• conferences
• teaching
• cooperation academia – industry
• new application areas
• funding
• organization
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Germany Chemical Society (GDCh)
Division “Chemical Information” changed to
“Chemical-Information-Computer (CIC)” in 1987
Workshop:
Software Development in Chemistry 1986-2004
German Conference on Chemoinformatics 2005
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Teaching
• define curriculum in chemoinformatics
• what contents of chemoinformatics have to go into regular chemistry curricula
Round Table + Committee
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Bioinformatics in Germany
Fachgruppe 4 der Gesellschaft für Informatik
(Division 4 of the Society for Informatics)
• definiton of a curriculum on Bioinformatics in 1990
• was then put on the web
all positions in bioinformatics at German universities were given to computer scientists
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Application Areas for Chemoinformatics
• drug design
• analytical chemistry
• chemical engineering
• inorganic chemistry
• medicinal chemistry
• organic chemistry
• physical chemistry
• theoretical chemistry
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Cooperation Industry - Academia
• industry: generate data
• academia: develop methods
provide academia access to data
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Funding
• increase awareness for importance of Chemoinformatics
• go into committees
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C3 Introduction into CI; SS 03/1st lecture© Gasteiger et al.
Get Organized!
Chemometrics Society
QSAR Society
FECS Working Party: Computational Chemistry
Chemoinformatics Society