Department of Computing Science, University of Alberta, Canada.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W633-40. doi: 10.1093/nar/gkq375. Epub 2010 May 11.
PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS is unique in its comprehensiveness, its capacity to evaluate X-ray, NMR and predicted structures as well as its ability to evaluate a variety of experimental NMR data. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods to evaluate both global and residue specific: (i) covalent and geometric quality; (ii) non-bonded/packing quality; (iii) torsion angle quality; (iv) chemical shift quality and (v) NOE quality. In particular, PROSESS uses VADAR for coordinate, packing, H-bond, secondary structure and geometric analysis, GeNMR for calculating folding, threading and solvent energetics, ShiftX for calculating chemical shift correlations, RCI for correlating structure mobility to chemical shift and PREDITOR for calculating torsion angle-chemical shifts agreement. PROSESS also incorporates several other programs including MolProbity to assess atomic clashes, Xplor-NIH to identify and quantify NOE restraint violations and NAMD to assess structure energetics. PROSESS produces detailed tables, explanations, structural images and graphs that summarize the results and compare them to values observed in high-quality or high-resolution protein structures. Using a simplified red-amber-green coloring scheme PROSESS also alerts users about both general and residue-specific structural problems. PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca.
PROSESS（蛋白质结构评估套件和服务器）是一个设计用于评估和验证通过 X 射线晶体学、NMR 光谱学或计算建模生成的蛋白质结构的网络服务器。虽然在过去的 20 年中已经开发了许多结构评估包，但 PROSESS 在其全面性、评估 X 射线、NMR 和预测结构的能力以及评估各种实验 NMR 数据的能力方面是独一无二的。PROSESS 集成了各种以前开发的、知名的和经过充分测试的方法，以评估全局和残基特异性：（i）共价和几何质量；（ii）非键/包装质量；（iii）扭转角质量；（iv）化学位移质量和（v）NOE 质量。特别是，PROSESS 使用 VADAR 进行坐标、包装、氢键、二级结构和几何分析，使用 GeNMR 计算折叠、穿线和溶剂能量学，使用 ShiftX 计算化学位移相关性，使用 RCI 关联结构流动性与化学位移，使用 PREDITOR 计算扭转角-化学位移一致性。PROSESS 还包含其他几个程序，包括 MolProbity 评估原子冲突，Xplor-NIH 识别和量化 NOE 约束违反，以及 NAMD 评估结构能量学。PROSESS 生成详细的表格、解释、结构图像和图形，总结结果并将其与高质量或高分辨率蛋白质结构中观察到的值进行比较。PROSESS 使用简化的红-琥珀-绿配色方案，还提醒用户注意一般和残基特异性的结构问题。PROSESS 旨在作为一种工具，可供结构生物学家和数据库管理员用于评估和验证新确定的蛋白质结构。PROSESS 可在 http://www.prosess.ca 免费获得。
