MolProbity: all-atom structure validation for macromolecular crystallography.
MolProbity: all-atom structure validation for macromolecular crystallography.
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DOI：
10.1107/s0907444909042073
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发表时间：
2010-01
期刊：
影响因子：
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通讯作者：
Richardson DC
中科院分区：
文献类型：
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作者：
Chen VB;Arendall WB 3rd;Headd JJ;Keedy DA;Immormino RM;Kapral GJ;Murray LW;Richardson JS;Richardson DC
MolProbity结构验证可以诊断出大分子晶体结构中的大多数局部错误，并有助于指导它们的修正。MolProbity是一个结构验证web服务，它为蛋白质和核酸在全球和局部水平上提供广谱的基于坚实基础的模型质量评估。它在很大程度上依赖于优化的氢位置和全原子接触分析所提供的功率和灵敏度，并辅以更新版本的共价几何和扭转角标准。一些局部修正可以在MolProbity中自动执行，所有诊断都以图表和图形形式呈现，有助于指导手动重建。x射线晶体学以蛋白质、核酸和越来越多的多种形式和状态的大型复合物的原子三维结构的形式提供了丰富的生物学上重要的分子数据。自动化的进步，从结晶到数据收集，从相位到模型构建再到精化，使得使用晶体学解决结构问题比以往任何时候都更容易。然而，尽管有这些改进，影响生物学解释的局部错误在低分辨率下普遍存在，甚至高分辨率结构几乎都包含至少一些局部错误，如拉马钱德兰异常值、翻转的支链蛋白侧链和不正确的糖包。对于晶体学家和最终用户来说，有简单可靠的方法来诊断和纠正这些结构中的错误是至关重要的。MolProbity是作者帮助解决这个问题的贡献，本文回顾了它的一般功能，报告了最近的增强和使用情况，并提供了证据，证明由此产生的改进现在对全局数据库产生了有益的影响。
MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.