Computational Drug Design Practical Syllabus, Notes & PYQ for GGSIPU PhD Pharmaceutical Chemistry Overview
PhD Pharmaceutical Chemistry
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Computational Drug Design Practical
1Visualization of small / Macro-molecule structure, drawing of small molecules, and optimization of a small molecule (ligand Preparation).
2Sequence Database: Swiss-Prot/Uniprot; Protein Database (PDB); Selection and optimization of the protein structure (Protein Preparation).
3Docking: Protein grid generation, small molecule docking, and analysis of docking results.
4Flexible protein docking: Induced fit docking.
5Covalent docking.
6Homology modeling generation; Model refinement and validation of the generated model.
7De-novo structure-based drug design: Combinatorial library design and Identification of potential molecule by virtual screening workflow.
8Pharmacophore generation and virtual screening of databases.
92D-QSAR, 3D-QSAR development for series of molecules by atom-based QSAR and Field-based QSAR techniques and ADME Toxicity predictions.
10Energy-based Pharmacophore (E-Pharmacophore) generation and Shape based virtual screening.
11Antibody modeling, model validation, Antigen-Antibody docking, or Protein-Protein Docking.
12Residue-scanning and associated property predictions, Cysteine scanning, Reactive hot spots prediction, and Affinity Maturation.
13Q.M.: Small molecule Geometry optimization, Single-point energy calculation, spectral (U.V./Visible, VCD, I.R., NMR, Raman), and molecular property calculation (HOMO and LUMO, molecular orbitals, density, potential).
14Molecular Dynamics Simulations and trajectory analysis.
15Chemoinformatics analysis of chemical database (Binary fingerprint analysis, Similarity search, Clustering, Scaffold decomposition)
Subject Details
Lab CodePPC-651
Lab Credits4