Description

Day-1, Lecture, Forenoon (11:00 am to 12 noon): Introductory session will be a couple of lectures introducing basic concepts like: 1) Molecular mechanics, force field and descriptor concepts. 2) Geometry optimization and conformation analysis. 3) Molecular docking (including methods and scoring functions). 4) Ligand binding free energy calculations. 5) de novo drug design (for structurally well-defined receptor targets). 6) Pharmacophore elucidation. 7) Combinatorial library design (including issues such as molecular similarity/diversity calculations, etc.). Day-1, Lab Session, Post lunch (1:30 to 4:00 pm): will be a detailed hands-on session on the fundamental initial steps of molecular modeling using Autodock, a suite of modeling programs of The Scripps Research Institute, CA, USA. The topics covered in this session: Drawing a molecule, energy minimization (optimization) of both small molecules/ligands and proteins, studying structure and bonding patterns of molecules, generation and analysis of conformation of molecules. Day-2, Lab Session - Forenoon (10:00 am to 12 noon): The participants will be guided through a tutorial session, which will provide an overview of several computational techniques and applications areas of importance in contemporary drug design programs. Day-2, Lab Session, Post lunch (1:30 to 4:00 pm): The participants will be given an exercise session, where each person will download a protein and a few ligands from some of the publicly available data sources and use them on Autodock for molecular docking and to analyze the results of docking energy calculations for estimating ligand binding interactions. Additional requirements: Basic knowledge of proteins and their structure, interest to learn and use a scientific software (http://autodock.scripps.edu). Also, mandatory attendance at Course Code: 153