| 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 |
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Molecular Modeling and Drug Designing
An in-depth understanding of molecular modeling and drug design principles and techniques, which can be helpful in various fields, including ... Show more
Instructor
Dr. Abdul Rajjak Shaikh 34 Students enrolled
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Molecular modeling and drug design is a field of study involving computational methods and technologies to identify and develop new drugs that can be used to treat various diseases. This course can provide several benefits to students, including:
– An in-depth understanding of molecular modeling and drug design principles and techniques, which can be helpful in various fields, including pharmaceutical research and development, biotechnology, and academic research.
– Exposure to cutting-edge computational tools and techniques that can predict the structures and functions of proteins and small molecules and evaluate their potential as drug candidates.
– An opportunity to conduct original research that contributes to molecular modeling and drug design and develop the skills and knowledge needed to pursue a career in this field.
– The ability to apply computational approaches to solve real-world biological problems and gain insights into diseases’ molecular basis and the mechanisms of drug action.
Overall, this course can provide students with a comprehensive understanding of the principles and applications of this field and can equip them with the skills and knowledge needed to pursue a successful career in this exciting and rapidly-growing area of science.
Who can apply for Training?
B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)
M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)
M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)
B. Pharmacy/M.Pharmacy
Module - 1 (2 months)
Module - 2 (4 months)
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Who can apply for Training:
B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)
M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)
M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)
B.Pharmacy/M.Pharmacy
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