| Lecture Slides: |
HTML, PDF: handouts [729.8 kb], notes [776.7 kb] |
| References: |
Introduction to Protein Structure - Second Edition; C. Branden & J. Tooze, Garland Publishing; ISBN: 0815323050 - good section on experimental methods in the back. |
| Foundations of Structural Biology; L. J. Banaszak, Academic Press; ISBN: 01207770022 - a little stronger on the refinement and temperature factor explanations, omits Bragg's law. |
| 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 |
| Home Work |
1) Find out about your structure's biological unit (from the PDB file or the EBI Macromolecule Server) and add the rotation matrices as well as the translation vectors to your project. Describe in a few sentences how the biological unit is assembled from the assymetric unit.
2) Work through the excellent X-Ray Crystallography tutorial maintained by Bernhard Rupp at the Lawrence Livermore National Laboratories. See if you can find the experimental information in your protein's PDB file. Also have a look at the NMR tutorial of the Chemistry Department at the University of Illinois at Chicago
3) Read the paper An analysis of the Protein Data Bank in search of temporal and global trends published in Bioinformatics, 15:807-831 (1999). |
| Lecture Slides: |
HTML, PDF format [61.1 kb] |
| References: |
Kabsch W. & Sander C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers, 22:2577-2637 (1983) |
| Colloc'h N. et al. Comparison of three algorithms for the assignment of secondory structure in proteins: the advantages of a consensus assignment Prot. Eng. 6: 377-82 (1993) |
| Honig B. Protein Folding: From the Levinthal Paradox to Structure Prediction J. Mol. Biol. 293: 283-93 (1999) |
| Moult J. The current state of the art in protein structure prediction Curr Opin in Biotech. 7: 422-27 (1996) |
| 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 |
| Project Status |
By now, the project pages should include the following information:
- basic biology of protein
- basic structure description with a few images highlighting the different secondary structure elements, het groups if present and the different chains if applicable
- information about the biological unit including the rotation matrix and translation vectors needed
- short summary of the experimental data as given in the PDB file beyond what the Structure Explorer Summary page provides
- analysis of structure neighbor sites for "surprising" neighbors (small RMSD, low seq. identity or seemingly very different functionality for example)
- find DSSP archive and link to pet protein's DSSP output, add PDB secondary structure assignment including a legend and compare the DSSP and PDB assignments.
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