The following links provide loads of information about validation:

• Review paper on validation (PDF file): GJ Kleywegt, "Validation of protein crystal structures" (Topical review), Acta Crystallographica, D56, 249-265 (2000). This discusses many quality criteria (mostly pertaining to X-ray crystal structures of proteins). If you are unable to access or download this PDF file, you can also have it E-mailed to you using this form!
  You may want to read this paper before you do the practical, especially if you missed Gerard's lecture(s). On the other hand, if you're a participant in a course, workshop or summer school, you may have received a copy of this paper as a hand-out.
  For a more general introduction to validation, request a copy of GJ Kleywegt, "On vital aid: the why, what and how of validation", Acta Crystallographica, D65, 134-139 (2009).
  If you are specifically interested in drug design, you may also want to request a copy of AM Davis, SJ Teague & GJ Kleywegt, "Applications and limitations of X-ray crystallographic data in structure-based ligand and drug design", Angewandte Chemie International Edition, 42, 2718-2736 (2003) or of the sequel, AM Davis, SA St-Gallay & GJ Kleywegt, "Limitations and lessons in the use of X-ray structural information in drug design", Drug Discovery Today, 13, 831-841 (2008).
• Glossary of terms - whenever you come across an unfamiliar technical term in this practical, check the glossary for a definition
• Links related to structural databases etc.

The following sites contain ready-made reports about (amongst other things) the quality of models that have been deposited in the Protein Data Bank:

• RCSB, PDBe and PDBj, the three access portals of the World-wide Protein Data Bank (wwPDB), each with their own set of tools and services. A small amount of validation-related information for every entry is available from these sites.
• PDBReport (CMBI) - a collection of quality reports, generated by the program WHAT IF, for all models that have been deposited in the PDB
  • explanation of the WHAT IF output - description of the various checks that WHAT IF carries out
  • discussion of the WHAT IF output - from a crystallographer's point of view
• PDBsum (EBI) - a collection of reports on all models that have been deposited in the PDB, including some quality checks as carried out by the program PROCHECK.
• EDS (Electron Density Server; Uppsala) - a collection of reports on many models from the PDB (for which experimental crystallographic data has been deposited) with a focus on the fit of the model to the data.
• Vivaldi, a service to analyse validation-related information of NMR models in the PDB (PDBe)
• Ramachandran server (Uppsala)
• Ramachandran server (Bangalore)

The following servers enable you to run all sorts of quality checks on models that you submit yourself:

• Structure validation central (JCSG) - runs PROCHECK, SFCHECK, PROVE, ERRAT, WASP, DDQ, WHATCHECK and PSQS
• ADIT server (RCSB) - runs PROCHECK, NUCheck and (if structure factors in mmCIF format are provided) SFCHECK
• MolProbity server (various checks; Duke)
• STAN (STructure ANalysis) server (Uppsala) - produces Ramachandran and "CA-Ramachandran" plots for proteins and Duarte-Pyle plots for nucleic acids. Moreover, it runs the program WASP to check if any water molecules could be small cations instead (Na+, Li+, Mg+2, Ca+2). It also runs the program CISPEP to investigate if any non-proline peptide bond that has been modelled as trans could in reality be cis.
• Verify3D server (fold; UCLA)
• ERRAT server (contacts; UCLA)
• Ramachandran server (Bangalore)
• RamPage server (Ramachandran server; Cambridge)
• VADAR server (Alberta, Canada)
• PARVATI server (anisotropic temperature factors; Washington)
• ANOLEA server (Atomic Non-Local Environment Assessment; Namur, Belgium)
• pdbcare (PDB CArbohydrate REsidue check; Heidelberg)
• TB Consortium Bias Removal Server (Texas A&M University) - generates maps that are as little biased as possible and calculates real-space fit values

If you want to learn a little bit more about macromolecular crystallography, try these links:

• Randy Read's course at the University of Cambridge
• Bernard Rupp's introductory course

If you want to check the links on this page, try this.

Latest update on 12 October, 2011.