BINF 731: Protein Structure Analysis

COURSE OUTLINE

      1. Complexity of protein structure and protein folding
      2. Methods for experimental determination of three-dimensional structure
        1. X-ray crystallography
        2. Neutron diffraction
        3. NMR
      3. Protein structure verification and validation
      4. Protein structural hierarchy
        1. Structural building blocks
        2. Secondary and supersecondary structures
        3. Ramachandran diagram
        4. Secondary structure assignment and prediction
      5. Protein structure classification
      6. Protein structure databases
      7. Protein models
        1. All-atom models
        2. Residue-based models
        3. Simplified residue alphabets
        4. Lattice models
      8. Protein visualization
      9. Protein modeling
        1. Ab initio methods (QM, DFT)
        2. Energy based methods (energy minimization, molecular dynamics, simulated annealing)
        3. Stochastic searches (Monte Carlo, genetic algorithms)
      10. Knowledge based protein modeling
        1. Comparative modeling
        2. Fold recognition
      11. Protein structure prediction and structural genomics
      12. Computational analysis of protein-protein, protein-DNA, and protein-ligand interactions.
      13. Structure-function relationship in proteins, computational mutagenesis.
      14. Protein engineering