Computer Aided Drug Design (CADD)
Computer Aided Drug Design (CADD) is an exciting and an integral tool which involves diverse discipline of both applied and basic biological research.
Course Goal
- The aspirant would be familiarised with Computer Aided Drug Design (CADD)
- The aspirant will have an in-depth overview over the state-of-the-art methods and techniques
- Will be able to understand, interpret and perform the biological calculations
Curriculum
Module: 1 Modern drug design: what requirements must a drug fulfill
Module: 2 What is CADD?
Module: 3: Molecular modeling and drug designing
- Molecular mechanics (MM)
- The concept of force field in MM
- Nonbonded interaction potential
- Force field energies
- Classification of force fields
- QM/MM methods
- Energy Minimization methods
- Conformational searching
- Conformations of biomacromolecules
- Systematic search methods
- Random search methods
- Genetic algorithms
- Distance geometry
Module: 4 Protein Modeling
- The protein data rank (PDB)
- Relationship between sequence and 3D structure of a protein
- Alignment of protein sequences
- needleman-Wunsch alignment method
- Multiple sequence alignments (MSA)
- Homology modeling of proteins
- Construction of the core
- Refinement of the homology model
- Model verification
- Comparison of various strategies in homology modeling
- Drug designing
- Molecular recognition
- Structure-based ligand design
- Molecular docking
- Virtual screening
- Structure-based pharmacophore generation
- Pharmacophore representation
- De Novo design of ligands
- Peptides and peptide analogs as drugs: Peptidomimetics
- Basic concepts of QSAE
- 2D-QSAR in drug design
- Principal component analysis (PCA)
- Partial least squares method (PLS)
- COMFA and COMSIA
- ADMET calculation
Module V: Pharmacovigilance Compliance-Planning Programs & Drug Risks Benefits
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