This practical is intended to introduce a number of publicly available tools that help you assess the reliability of structural models. Assessing the quality of a model is called validation. Validation is something that needs to be done both by producers (crystallographers, NMR spectroscopists, electron microscopists, etc.) and users (biologists, enzymologists, medicinal chemists, etc.) of models. Note that we talk of models rather than structures, since a model is just a simplified representation of a human being's hypothesis of what a molecule looks like (a collection of point atoms, often even ignoring hydrogen atoms).

In this practical, we will focus mainly on validation of protein models determined using crystallographic data. This does not mean that NMR models are more reliable a priori (au contraire), or that nucleic acid models need no validation (au contraire). Fortunately, many coordinate-based quality checks can be applied equally well to NMR as to X-ray models, and some apply just as much to nucleic acid models as they do to protein models.

Upon successful completion of this practical, you should be able to:

• read papers about protein crystal structures (errr, models) and understand the discussion of the model's quality (and ask relevant questions on this subject after hearing a protein crystallographer give a talk on a particular structure, or after reading a manuscript that you are to referee)

• find or generate quality-related information on a given protein model using web-based databases and servers

• use this information to form a general opinion as to the overall quality of the model, as well as of certain aspects of it (e.g., the extent to which the presence or conformation of a bound ligand is supported by the crystallographic data)

• select the better of a set of related models (assuming there are noticeable differences in the quality of these models), e.g. for purposes of homology modelling, ligand design, mutant design, or molecular replacement calculations

To do this practical you will need a molecular graphics program or plug-in that allows you to look at protein structures, identify atoms and residues, etc. A simple program such as RasMol is fine (check here if you have Rasmol installed and if your browser is configured appropriately), but O, SwissPDBViewer, PyMol, Coot, etc. will also do fine. Check which graphics programs are installed on the computer you are using and pick the one that you are most familiar with.

Also, if you want to make full use of the Uppsala Electron Density Server (EDS) during this practical, you will need to have access to (and some experience with) the program O (this only applies to [aspiring] crystallographers). (Note that some other programs also provide direct links to EDS data, e.g., PyMol, Chimera and Coot). If you have Java installed you will also be able to use the density viewers provided by EDS. To test if this works properly, click this link; after a little while you should see something like this.

A set of links that is particularly relevant to this practical can be found here. Check this page out before you continue with the practical!

If you have previously started with this tutorial and wish to continue, select the section with which you want to continue from the pop-up menu below and then hit the "Go!" button. Otherwise just click the "Next" button below.

History ...

1. Practical by Gerard Kleywegt, Uppsala University.
   Developed for the 2001 EMBO Bioinformatics course in Uppsala.
2. Updated for the 2002 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
3. Updated for the 2002 course in X-ray Crystallography in Uppsala.
4. Updated for the 2002 BioCrys course on Basic Crystallography in Oeiras, Portugal.
5. Updated for the 2002 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
6. Updated for the 2003 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
7. Updated for the 2003 course in X-ray Crystallography in Uppsala.
8. Updated for the 2003 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
9. Updated for the 2004 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
10. Updated for the 2004 course (March) in X-ray Crystallography in Uppsala.
11. Updated for the 2004 EMBO lecture course on "3D Structure Databases - Uses for Biological Problem solving" in Cambridge, UK.
12. Updated for the 2004 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
13. Updated for the 2004 course (December, this time) in X-ray Crystallography in Uppsala.
14. Updated for the 2005 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
15. Updated for the one-day workshop on Validation in Sao Paulo, Brazil, 1 July, 2005.
16. Updated for the 2005 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
17. Updated for the 2005 course in X-ray Crystallography in Uppsala.
18. Updated for the 2006 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
19. Updated for the 2006 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
20. Updated for the 2006 course in X-ray Crystallography in Uppsala.
21. Updated for the 2007 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
22. Updated for the 2007 course in X-ray Crystallography in Uppsala.
23. Updated for the 2008 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.
24. Updated for the 2008 Cold Spring Harbor Macromolecular Crystallography Course in Beijing (China).
25. Updated for the 2008 Macromolecular Crystallography Course in Cold Spring Harbor (NY).
26. Updated for the 2008 course in X-ray Crystallography in Uppsala.
27. Updated for the 2009 Ph.D. course in Protein Crystallography in Copenhagen, Denmark.

Latest update on 26 January, 2009.