Post on 19-Dec-2015
Drug DockingDrug Docking
Computer Science Computer Science DepartmentDepartment
Brigham Young UniversityBrigham Young University
Andrew HarrisAndrew Harris
Mark ClementMark Clement
Kenneth SundbergKenneth Sundberg
Genetic DiseaseGenetic Disease
Some diseases caused by over-Some diseases caused by over-expression/under-expression of expression/under-expression of certain proteins or enzymes in a given certain 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 Process
1.1. Find Targets, Inhibitors, Find Targets, Inhibitors, CompoundsCompounds
2.2. Experiment Drug CandidatesExperiment Drug Candidates
3.3. 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
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