Protein Structure Modeling Third Semester Syllabus for MSc Bioinformatics
COURSE NAME: Protein Structure Modeling
COURSE CODE: BIF559
PROGRAM: MSc Bioinformatics
Complexity of protein structure and protein folding, Methods for experimental determination of three-dimensional structure - X-ray crystallography, Neutron diffraction, NMR; Protein structure verification and validation; Protein structural hierarchy -Structural building blocks, Secondary and supersecondary structures, Ramachandran diagram, Secondary structure assignment and prediction; Protein structure classification; Protein structure databases; Protein models -All-atom models, Residue-based models, Simplified residue alphabets, Lattice models; Protein visualization; Protein modelling -Ab initio methods (QM, DFT), Energy based methods (energy minimization, molecular dynamics, simulated annealing), Stochastic searches (Monte Carlo, genetic algorithms); Knowledge based protein modelling- Comparative modelling, Fold recognition; Protein structure prediction and structural genomics; Computational analysis of protein-protein, protein-DNA, and protein-ligand interactions; Structure-function relationship in proteins, computational mutagenesis; Protein engineering
- Arthur M. Lesk, Introduction to Protein Architecture : The Structural Biology of Proteins Oxford: Oxford University Press, 2000. xii, 347 p.
- Philip Bourne, HelgeWeissig (Editors), Structural bioinformatics, Hoboken, N.J. : Wiley-Liss, 2003. xix, 649 p.