Schedule and Materials for Computational Drug Discovery

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Paper presentations should be sent within a few days of class, if not before, so they can be posted here. My own slides are now posted alongside their topic rather than date, so most slides are listed with the class immediately after they were actually shown.

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Date Topic Notes and Slides (pdf) Readings Paper Presentations (ppt)

Jan. 10 History and Introduction Notes, Slides -- --

Jan. 17 Searches, Pharmacophores, and QSAR Notes, Slides RAPID: Randomized Pharmacophore Identification for Drug Design - ps / lower res. pdf (Finn, Latombe, Motwani, Yao, et. al.),
Identification of... Growth Hormone Secretagogue Agonists by Virtual Screening and Structure-Activity Relationship Analysis... (J. Med. Chem.),
QSAR analysis of anticonvulsant agents using k nearest neighbor and simulated annealing PLS methods (J. Med. Chem.)
Kiran, Greg, Dylan

Jan. 24 Docking Notes, End of prev. week's slides Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine (Jain, J. Med. Chem.),
Ligand-Based Structural Hypotheses for Virtual Screening (Jain, J. Med. Chem.),
A Critical Assessment of Docking Programs and Scoring Functions (Warren, et. al., J. Med. Chem.)
Susan, Dariya, Julia

Jan. 31 Molecular Mechanics and Dynamics Notes, Slides Dissociation of an antiviral compound from... human rhinovirus 14 capsid (Li, et. al, PNAS)
LINCS: A linear constraint solver for molecular simulations (Hess, et. al., J.C.C.)
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs (Perryman, et. al., Prot. Sci.)
Richard, Ankur, Ankit

Feb. 7 Free Energy Computation Notes, Slides Hierarchical Database Screenings for HIV-1 RT Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM-PB/SA (Junmei Wang, et. al., J. Med. Chem.)
Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues (Archontis, et. al., Proteins)
Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field (Grossfield, et. al., JACS)
Stochastic roadmap simulation for the study of ligand-protein interactions (Apaydin, et. al., Bioinformatics)
Susan, Pratik, Gaurav, Max

Feb. 14 Library Design Notes, Slides Combinatorial Library Design Using a Multiobjective Genetic Algorithm (Gillet, et. al.)
Novel Dihydrofolate Reductase Inhibitors. Structure-Based versus Diversity-Based Library Design and High-Throughput Synthesis and Screening (Wyss, et. al.)
Luddite: An Information-Theoretic Library Design Tool (Miller, et. al.)
Greg, Kiran, David

Feb. 21 Designing Small Molecules Notes, Slides Combinatorial computational method gives new picomolar ligands for a known enzyme (Grzybowski, et. al.)
BREED: Generating Novel Inhibitors through Hybridization of Known Ligands. Application to CDK2, P38, and HIV Protease (Pierce, Road, and Bemis)
CONCERTS: Dynamic Connection of Fragments as an Approach to de Novo Ligand Design (Pearlman and Murcko)
A genetic algorithm for structure-based de novo design (Pegg, Haresco, and Kuntz)
Dylan, Richard, Adam, Pratik

Feb. 28 Beyond Binding: In silico ADME Notes, Slides Predicting Blood-Brain Barrier Permeation from Three-Dimensional Molecular Structure (Crivori, et. al.)
Validation of Model of Cytochrome P450 2D6: An in Silico Tool for Predicting Metabolism and Inhibition (Kemp, et. al.)
Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs (Vieth, et. al.)
Ankit, Inbal, Julia

Mar. 7 Computational Infrastructures Notes, Slides Building and managing production bioclusters (Dagdigian)
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations (Taiji, et. al.)
Introduction to the Cell multiprocessor (Kahle, et. al.)
Ankur, David, Max

Mar. 14 Case Studies Case presentations

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Date	Topic	Notes and Slides (pdf)	Readings	Paper Presentations (ppt)
Jan. 10	History and Introduction	Notes, Slides	--	--
Jan. 17	Searches, Pharmacophores, and QSAR	Notes, Slides	RAPID: Randomized Pharmacophore Identification for Drug Design - ps / lower res. pdf (Finn, Latombe, Motwani, Yao, et. al.), Identification of... Growth Hormone Secretagogue Agonists by Virtual Screening and Structure-Activity Relationship Analysis... (J. Med. Chem.), QSAR analysis of anticonvulsant agents using k nearest neighbor and simulated annealing PLS methods (J. Med. Chem.)	Kiran, Greg, Dylan
Jan. 24	Docking	Notes, End of prev. week's slides	Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine (Jain, J. Med. Chem.), Ligand-Based Structural Hypotheses for Virtual Screening (Jain, J. Med. Chem.), A Critical Assessment of Docking Programs and Scoring Functions (Warren, et. al., J. Med. Chem.)	Susan, Dariya, Julia
Jan. 31	Molecular Mechanics and Dynamics	Notes, Slides	Dissociation of an antiviral compound from... human rhinovirus 14 capsid (Li, et. al, PNAS) LINCS: A linear constraint solver for molecular simulations (Hess, et. al., J.C.C.) HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs (Perryman, et. al., Prot. Sci.)	Richard, Ankur, Ankit
Feb. 7	Free Energy Computation	Notes, Slides	Hierarchical Database Screenings for HIV-1 RT Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM-PB/SA (Junmei Wang, et. al., J. Med. Chem.) Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues (Archontis, et. al., Proteins) Ion Solvation Thermodynamics from Simulation with a Polarizable Force Field (Grossfield, et. al., JACS) Stochastic roadmap simulation for the study of ligand-protein interactions (Apaydin, et. al., Bioinformatics)	Susan, Pratik, Gaurav, Max
Feb. 14	Library Design	Notes, Slides	Combinatorial Library Design Using a Multiobjective Genetic Algorithm (Gillet, et. al.) Novel Dihydrofolate Reductase Inhibitors. Structure-Based versus Diversity-Based Library Design and High-Throughput Synthesis and Screening (Wyss, et. al.) Luddite: An Information-Theoretic Library Design Tool (Miller, et. al.)	Greg, Kiran, David
Feb. 21	Designing Small Molecules	Notes, Slides	Combinatorial computational method gives new picomolar ligands for a known enzyme (Grzybowski, et. al.) BREED: Generating Novel Inhibitors through Hybridization of Known Ligands. Application to CDK2, P38, and HIV Protease (Pierce, Road, and Bemis) CONCERTS: Dynamic Connection of Fragments as an Approach to de Novo Ligand Design (Pearlman and Murcko) A genetic algorithm for structure-based de novo design (Pegg, Haresco, and Kuntz)	Dylan, Richard, Adam, Pratik
Feb. 28	Beyond Binding: In silico ADME	Notes, Slides	Predicting Blood-Brain Barrier Permeation from Three-Dimensional Molecular Structure (Crivori, et. al.) Validation of Model of Cytochrome P450 2D6: An in Silico Tool for Predicting Metabolism and Inhibition (Kemp, et. al.) Characteristic Physical Properties and Structural Fragments of Marketed Oral Drugs (Vieth, et. al.)	Ankit, Inbal, Julia
Mar. 7	Computational Infrastructures	Notes, Slides	Building and managing production bioclusters (Dagdigian) Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations (Taiji, et. al.) Introduction to the Cell multiprocessor (Kahle, et. al.)	Ankur, David, Max
Mar. 14	Case Studies			Case presentations