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Computational Structural Bioinformatics: Winter 2024
Sample Exam
Resources
Books and Review articles
1) Protein Structure:
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Introduction to Protein Structure, Branden, C. and Tooze, J. (1991)
Garland Publishing, New York
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Proteins, Creighton, T.E. (1993) 2nd edition, W.H. Freeman & Co.,
New York
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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
- 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
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