Computational Structural Bioinformatics: Winter 2024

Sample Exam

Resources

Books and Review articles

1) Protein Structure:

• Introduction to Protein Structure, Branden, C. and Tooze, J. (1991) Garland Publishing, New York
• Proteins, Creighton, T.E. (1993) 2nd edition, W.H. Freeman & Co., New York
• Principles of Protein Structure, Schulz, G.E. and Schirmer, R.H. (1979) Springer-Verlag, New York


• Chothia, C., Levitt, M. and Richardson, D. (1977) Structure of proteins: Packing of alpha helices and beta sheets Proc. Natl. Acad. Sci. USA 74 4130-4134
• Chothia, C. (1984) Principles that determine the structure of proteins Ann. Rev. Biochem. 53 537-572
• Lesk, A.M. (1991) Protein architecture : a practical approach, IRL press, Oxford
• Rao, S.T. and Rossman, M.G. (1973) Comparison of super-secondary structures in proteins J. Mol. Biol. 76 241-256
• Richardson, J.S. (1981) The anatomy and taxonomy of protein structure Adv. Prot. Chem. 34 167-339
• Chothia, C, Hubbard, T, Brenner, S, Burns, H and Murzin, A. (1997) Protein folds in the all-beta and all-alpha classes Annu. Rev. Biophys. Biomol. Struct. 26 597-627
• Chao Zhang and S.H. Kim (2000) The anatomy of protein beta-sheet topology J. Mol. Biol. 299 1075-1089
• Chao Zhang and S.H. Kim (2000) A comprehensive analysis of the greek key motifs in protein beta-barrels and beta-sandwiches Proteins: Struct. Func. Genet. 40 409-419

2) Protein Structure Classification and Prediction

• Taylor, WR, May, ACW, Brown, NP and Aszodi, A (2001) Protein structure: geometry, topology and classification Rep. Prog. Phys. 64 517-590
• Ouzounis, CA, Coulson, RMR, Enright AJ, Kunin, V and Pereira-Leal, JB. (2003) Classification schemes for protein structure and function Nature Genetics 4 509-519
• Handout on Protein Structure Classification : PDF_file

Useful links

• Databases
  
  • the Protein Data Bank (PDB)
• Visualization programs
  
  • RasMol
  • PyMol:
    • Information for free license for education: here
      If you fill in the form, you should receive an email from Schoedinger, with a username, a password, and a link from which you will be able to download the version of Pymol for your operating system. This is really useful, especially on Windows systems.
    • Specific information for Windows: here. This is really useful if you want to install the open source version of pymol.
    • Specific option for Mac OS X: Using brew to install pymol
    • Linux install of pymol: Info
  • Kinemage
  • Ramachandran Plot Explorer
• Protein Structure
  
  • Amino Acids (quizzes, ....)