Syllabus
Introduction – Structure – Properties – Molecular Formats – SMILES – SMART – Mol – SDF – InChi – Molecular Representation – Chemsketch – Chemistry -42 – Automated De Novo Design – Scalable Engineering of Chemistry – Databases – Pubchem – Drug Bank – ZINC – ADME Constrains – Forcefields – Molecular Mechanics – Quantum Mechanics – Configurations – Boundaries – Confirmations – QSAR – Hansch Equation – Free Wilson Method – CoMFA – CoMSIA – Ligand – Based Drug Design –Molecular Annotation- Pharmacopore – Structure-Based Drug Design – Free-Energy Binding Analysis – 3-D Modeling – Proteins – Pharma AI – Panda Omics: Disease-Target Identification – Synthetic Biology – Prediction – In Clinico: Clinical Outcomes – Chemistry 42: Novel Lead Molecules -Virtual Screening – Docking – MD Simulation.
Objectives and Outcomes
Course Objectives
- The course will lay down the basic concepts of computational techniques to analyse the coordinate systems in molecular construction.
- It will explore the concepts initially through basic formats to represent synthetic and biomolecules.
- It will provide an appreciation for the broad application of AI in drug design.
- Goal of the course is to provide a connection between the concepts of organic chemistry and simulation studies.
Course Outcomes
After completing this course, students will be able to
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To develop an understanding of the basic concepts of Machine Learning Techniques in Computer Aided Drug Design.
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To evaluate the suitability of molecular file formats in 2-D and 3-D analysis.
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To connect the concepts of 2-D and 3-D Modeling of Synthetic and Biomolecules.
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To evaluate the biologically active point of biomolecular confirmations.
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Text Books / References
Textbooks / References
- Raman (2021) An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks, Chapman and Hall/CRC, Boca Raton, FL.
Voit E (2012) A First Course in Systems Biology, Garland Science.
Klipp E (2009) Systems Biology, A Textbook, Wiley-VCH.
Newman MEG (2011), “Networks: An Introduction”, Oxford University Press.
Weblink:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/computer-aided-drug-design
Weblink: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5248982/
Weblink: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0351-x
Weblink: https://www.frontiersin.org/articles/10.3389/fchem.2018.00057/full
Weblink: https://insilico.com/chemistry42
