DESCRIPTION OF COURSES

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BI 523 ADVANCED TECHNIQUES FOR SEQUENCE AND STRUCTURE ANALYSIS                               (1L+2P) I

Objective
  To teach various approaches meant for sequence alignment and docking simulation in proteomics.

Theory

UNIT I
  Advanced Techniques for Sequence Analysis: Sequence Profiles: Derivation, Databases, Application, Gapped BLAST, PSI-BLAST, PHI-BLAST;

UNIT II
  Advanced Techniques for Structure Analysis: Molecular replacement method, Direct method & Fiber diffraction, Methods for Comparison of 3D structures; Application of the optimization techniques: Sequence Alignments, Prediction of Protein Structure, Docking Simulations; Advance techniques in Prediction of 3D Structure: Rossetta Stone Hidden Markov Model, Neural networks.

UNIT III
  Molecular Dynamics Simulations & Monte Carlo Methods: Electrostatics of  biomolecules, Simulations of Bio-macromolecular Structures in Water & membrane, Free energy perturbation method; Simulated Annealing: Multiple Sequence Alignments, Simulations of Bio-macromolecular Structures; Designing of molecules like drug, inhibitors using: Structure based and ligand based docking methods, Different Scoring schemes.

Practicals
  Advanced Techniques for Sequence Analysis, Molecular replacement method, Methods for Comparison of 3D structures, Optimization techniques: Sequence Alignments, Prediction of Protein Structure, Docking Simulations; Advance techniques in Prediction of 3D Structure.

Suggested Readings