Evaluating protein structures determined by structural genomics consortia.

摘要: Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality these data, we have developed protein structure validation software suite (PSVS), assessment structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable in biology projects. The integrates under a single interface analyses from several widely-used evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283-291), MolProbity (Lovell Proteins 2003;50:437-450), Verify3D (Luthy Nature 1992;356:83-85), ProsaII (Sippl, 1993;17: 355-362), PDB software, and various structure-validation tools our own laboratory. provides standard constraint analyses, statistics on goodness-of-fit between experimental knowledge-based scores standardized format suitable database integration. analysis both global site-specific measures quality. Global reported as Z scores, based calibration with set high-resolution crystal structures. particularly useful assessing determined methods, but also valuable homology models. Using assessed Northeast Genomics Consortium other international projects, over 5-year period. Protein produced exhibit score distributions similar to those traditional during same time However, while some seen higher-resolution structures, majority lower scores. Potential reasons this "structure gap" discussed.