drug docking
DESCRIPTION
Drug Docking. Andrew Harris Mark Clement Kenneth Sundberg. Computer Science Department Brigham Young University. Trypsinogen. Trypsin. Chymotrypsinogen. Chymotrypsin. Enterokinase. Duodenal Cell. Genetic Disease. - PowerPoint PPT PresentationTRANSCRIPT
Drug DockingDrug Docking
Computer Science Computer Science DepartmentDepartment
Brigham Young UniversityBrigham Young University
Andrew HarrisAndrew HarrisMark ClementMark Clement
Kenneth SundbergKenneth Sundberg
Trypsinogen
Trypsin
Chymotrypsinogen
Chymotrypsin
Duodenal Cell
Enterokinase
Genetic DiseaseGenetic Disease Some diseases caused by over-Some diseases caused by over-
expression/under-expression of certain expression/under-expression of certain proteins or enzymes in a given proteins or enzymes in a given pathwaypathway
Down Syndrome – Trisomy 21, extra Down Syndrome – Trisomy 21, extra 2121stst chromosome chromosome Larger oral-pharyngeal anatomyLarger oral-pharyngeal anatomy Smaller jawSmaller jaw Learning disabilityLearning disability
Theoretically treatable with drugsTheoretically treatable with drugs
Drug Design ProcessDrug Design Process1.1. Find Targets, Inhibitors, Find Targets, Inhibitors,
CompoundsCompounds2.2. Experiment Drug CandidatesExperiment Drug Candidates3.3. Validate Validate in vitroin vitro
InformationInformation ZINC, Human Genome Project now ZINC, Human Genome Project now
make this sequence information make this sequence information availableavailable
Reduce time sifting through, predict Reduce time sifting through, predict side effectsside effects
PyMOLPyMOL A molecular graphics visualization toolA molecular graphics visualization tool Embedded Python interpreterEmbedded Python interpreter Open SourceOpen Source
Drug Docking AlgorithmDrug Docking Algorithm SearchingSearching
SuperpositionSuperposition RotationRotation
ScoringScoring Root Mean Square Deviation (RMSD)Root Mean Square Deviation (RMSD) Bond EnergiesBond Energies
SearchingSearching Centroid Calculation, Geometric Centroid Calculation, Geometric
TranslationTranslation Matrix Multiplication RotationMatrix Multiplication Rotation
ScoringScoring
Translation,Rotation
Least RMSD score
Drug Docking AlgorithmDrug Docking Algorithm
transpose centroids to the origintranspose centroids to the origin foreach angular displacement in xforeach angular displacement in x
foreach angular displacement in yforeach angular displacement in y foreach angular displacement in zforeach angular displacement in z
Calculate RMSDCalculate RMSD If this RMSD is less than current minimum, save itIf this RMSD is less than current minimum, save it
Simple 3D Superposition Simple 3D Superposition and Alignmentand Alignment
Modified AlgorithmModified Algorithm
Modified for Drug Modified for Drug DockingDocking
Biotin Docking to Biotin Docking to StreptavidinStreptavidin
Questions?Questions?