| Lecture Slides: |
HTML, PDF format |
References: |
Crystallography |
Practical Protein Crystallography; D. E. McRee, Academic Press; ISBN: 0124860508 - focusses strongly on XtalView, a comprehensive software package developed by the author. Good and clear definitions of important terms. |
| Crystallography Made Crystal Clear: A Guide for User's of Macromolecular Models ; G. Rhodes, Academic Press; ISBN: 0125870728 - very good, comprehensive text. A little thin on the mathmatics... might be a plus :) |
X-Ray Crystallography tutorial by Bernhard Rupp |
| Weissig H, Bourne PE. An analysis of the Protein Data Bank in search of temporal and global trends in Bioinformatics, 15:807-831 (1999). |
| Structure based Functional Assignments |
SITE/Site Match: Zhang B, Rychlewski L, Pawlowski K, Fetrow JS, Skolnick J, Godzik A. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein Sci. 1999 May;8(5):1104-15. |
| TESS: Wallace AC, Borkakoti N, Thornton JM. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 1997 Nov;6(11):2308-23. |
| Fuzzy Functional Forms: Fetrow JS, Siew N, Di Gennaro JA, Martinez-Yamout M, Dyson HJ, Skolnick J. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Sci. 2001 May;10(5):1005-14. |
| SPASM & RIGOR: Kleywegt GJ. Recognition of spatial motifs in protein structures. J Mol Biol. 1999 Jan 29;285(4):1887-97.
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| Mol. Recognition: Kobayashi N, Go N. A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur Biophys J. 1997;26(2):135-44. |
| Prot. Side Chain Patterns: Russell RB. Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution. J Mol Biol. 1998 Jun 26;279(5):1211-27. |
| Project Status |
The following sections should be part of your project by next week:
- Basic introduction on your protein including 2 or 3 Rasmol images. You might want to highlight any ligands.
- A section on the secondary structure assignment as per PDB or dssp
- SCOP & CATH classifications including some descriptive text. Please look at functional annotations for members of the same family or superfamily. Is there any conservation of function? Are there any analogues with the same function?
- Experimental details including resolution, R-factor, crystal unit cell dimensions and space group. Add any relevant information from the PDB files experimental details section.
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| Lecture Slides: |
HTML, PDF format |
| References: |
Godzik A. The structural alignment between two proteins: is there a unique answer? Protein Sci. 5:1325-38 (1996) |
| Holm L & Sander C: Searching protein structure databases has come of age. Proteins 19:165-73 (1994) |
| Gibrat JF, et al. Surprising similarities in structure comparison. Curr Opin Struct Biol. 6:377-85 (1996) |
| Shindyalov IN & Bourne PE Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:739-47 (1998) |
| Honig B. Protein Folding: From the Levinthal Paradox to Structure Prediction J. Mol. Biol. 293: 283-93 (1999) |
- Venclovas, Zemla A, Fidelis K, Moult J. Comparison of performance in successive CASP experiments. Proteins. 45 Suppl 5:163-70.(2001)
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| Koehl P. & Levitt M. A brighter future for protein structure prediction Nat. Struct. Biol. 6: 108-11 (1999) |
| Protein Structure Prediction - A practical approach; M. J. E. Sternberg (ed.), IRL Press; ISBN: 0199634963 - published in 1996, this book is still a good and comprehensive overview of the field, including sequence alignment searches, secondary structure prediction and ligand docking |
| Li WW, Reddy BV, Tate JG, Shindyalov IN, Bourne PE. CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Res. 30:409-11. (2002) |
| Project Status |
The following items should be added to your project:
- A list of structural neighbors of your protein
- A multiple sequence alignment output of these structures generated by ClustalW
- A comparison between the structural and sequence relationships
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