MolProbity: More and better reference data for improved all-atom structure validation
MolProbity: More and better reference data for improved all-atom structure validation
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DOI：
10.1002/pro.3330
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发表时间：
2018-01-01
期刊：
影响因子：
8
通讯作者：
Richardson, David C.
中科院分区：
文献类型：
--
作者：
Williams, Christopher J.;Headd, Jeffrey J.;Richardson, David C.
本文介绍了MolProbity网站上提供的大分子模型验证服务的当前更新，强调了自2010年上次审查以来的变化和补充。已经有许多基础设施的改进，包括重写以前的Java实用程序，现在使用现有的或新编写的Python实用程序在开源的CCTBX部分的凤凰软件系统。这提高了长期的可维护性，并增强了Phenix中MolProbit风格验证的全面集成。现在有一个完整的MolProbity镜像站点。GitHub提供我们的开源代码，参考数据集以及定义大多数验证标准的多维分布。Asn/Gln/His翻转校正后的坐标输出现在更加理想化，因为过去显然经常跳过后细化步骤。两组不同的重原子到氢的距离和伴随的货车德瓦耳斯半径已被研究和改进的精度，一个电子云中心的位置适合于X射线晶体学和一个核的位置。新的验证包括在输入时关于引起问题的格式不规则性的消息，来自新参考数据集中的百万质量过滤残基的Ramachandran和旋转异构体标准的更新，用于cryoEM或低分辨率X射线的骨架和二级结构的CaBLAM C-CO虚拟角度分析，以及最近被过度使用的非常罕见的顺式-非脯氨酸和扭曲肽的标记。由于MolProbity验证和校正的广泛应用，在Phenix和全球蛋白质数据库中，新沉积的结构继续得到极大的改善，这是由MolProbity独特的全原子clashscore测量的。
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at . GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His flip correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM C-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.