| Module – I (2 months) | Ligand based drug design (Pharmacophore design) |
| Topics | -Introduction and Background -Understanding different file formats (sdf,mol2,pdb) -SMILES/canSMILE -Collection of primary key data -Pharmacophore preparation -Chemical Library preparation based on Pharmacophore -Insilico Screening (ADME) -Toxicity screening – QSAR(Quantitative structure-activity relationship) Databases – Pubchem, Drugbank, ZincPharmar etc -Tools – OpenBabel, Discovery Studio, KNIME, Marvin Sketch, and others (suggestions) etc |
| Module – II (4 months) | Structure based drug design (target-ligand docking) |
| Topics | – Introduction to drug designing – Data mining, literature study and acquisition of target structure Databases- NCBI, PDB, RCSB, UNIPROT, Modbase – Comparative modeling of protein (Homology modeling) *target structure not available – Server based –PHYRE, RaptorX, SWISSMODEL, I-TASSER etc – Software based–Modeller(standalone) – Protein structure validation – Ramachandran plot assessment –RAMPAGE,Pdbsum , Procheck and Profiles3d – Molecular Docking (AutoDockTools)(file to file command explanation) – Active site Pocket identification -MetaPocket, CastP etc – Protein and ligand preparation – Setting grid parameters and Docking parameters -Setting up docking on command line -Docking analysis (based on binding energy, Hydrogen bonds, electrostatic interaction, hydrophobic interaction etc) -ADT (*Auto Dock vina for multiple ligands) -BINANA (BINding ANAlyser) – Pdbsum Building protein-ligand complex and visualization |