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BI 511 RNA/PROTEIN STRUCTURE PREDICTION AND MOLECULAR MODELING                                                                                 (1L+2P) III

Objective
  To get insight into various techniques and tools available for protein structure prediction, visualization and validation.

Theory

UNIT I
  Structural data, databases and structure analysis: Exploring the Database searches on PDB and CSD, WHATIF Molecular visualization tools; Visualization of tertiary structures, quaternary structures, architectures and topologies of proteins and DNA using molecular visualization softwares such as RasMol, Cn3D, SPDBV, Chime, Mol4D etc.

UNIT II
  Structure prediction tools and homology modeling: Prediction of secondary structures of proteins using different methods with analysis and interpretation of  the results; Comparison of  the performance of the different methods for various classes of proteins. (Fasman method, Garnier Osguthorpe Robson (GOR), Neural Network based; methods); NLP approach for secondary structure prediction of RNA; Introduction to mfold and Vienna packages; Prediction of tertiary structures of proteins using Homology Modeling approach: SWISSMODEL, SWISS-PDB Viewer; Prediction of tertiary structures of proteins different methods for fold recognition along with analysis and interpretation of results (Threading techniques; Homology Modeling and abinitio methods).

UNIT III
  Molecular dynamics simulation and docking: Basic principles of theoretical modeling, Empirical force fields for biomolecular simulations, Energy minimization, Molecular dynamics, Monte Carlo simulation Peptide building (PYMOL / DStools ).

Practicals
  Structural data, databases and structure analysis, Molecular visualization tools, Structure prediction tools and homology modeling, Molecular dynamics simulation and docking

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