The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites.
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DOI：
10.1186/1758-2946-5-36
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发表时间：
2013-07-29
影响因子：
8.6
通讯作者：
Pujadas G
中科院分区：
文献类型：
--
作者：
Cereto-Massagué A;Ojeda MJ;Joosten RP;Valls C;Mulero M;Salvado MJ;Arola-Arnal A;Arola L;Garcia-Vallvé S;Pujadas G
许多蛋白质数据库（PDB）的用户认为，存放的结构模型是高质量的，但忘记了这些模型是来自实验数据的解释。原子坐标的准确性在模型之间或在同一模型中是不均匀的。为了避免基于一个有缺陷的模型的研究项目，我们提出了一个工具，用于评估质量的配体和结合位点的晶体学模型从PDB。用于配体和结合位点的验证HElper（VHELIBS）是一种软件，旨在简化非晶体学家（即，具有很少或没有晶体学知识的用户）。使用一个方便的图形用户界面，它允许一个检查如何配体和结合位点坐标适合电子密度图。VHELIBS可以使用来自重新细化和重新构建的晶体学模型的PDB或PDB_REDO数据库的模型。用户可以为与坐标与电子密度的拟合相关的一系列属性指定阈值（默认使用真实的空间R、真实的空间相关系数和平均占有率）。VHELIBS将根据规定的限度自动将残留物和配体分类为良好、可疑或不良。用户还能够目视检查残基和配体与电子密度图的拟合质量，并在需要时对其进行重新分类。VHELIBS允许没有经验的用户检查结合位点和配体坐标与实验数据的关系。这是一个重要的步骤，以评估其适合药物发现的目的，如基于结构的药效团开发和蛋白质配体对接实验模型。
Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB. The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed. VHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments.
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DOI：
10.1107/s0907444910045749
发表时间：
2011-04
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Winn MD;Ballard CC;Cowtan KD;Dodson EJ;Emsley P;Evans PR;Keegan RM;Krissinel EB;Leslie AG;McCoy A;McNicholas SJ;Murshudov GN;Pannu NS;Potterton EA;Powell HR;Read RJ;Vagin A;Wilson KS
通讯作者：
Wilson KS
影响因子：
5.8
作者：
Joosten, Robbie P.;Joosten, Krista;Perrakis, Anastassis
通讯作者：
Perrakis, Anastassis
DOI：
10.1107/s0907444912044423
发表时间：
2013-02-01
影响因子：
2.2
作者：
Pozharski, Edwin;Weichenberger, Christian X.;Rupp, Bernhard
通讯作者：
Rupp, Bernhard
影响因子：
5.6
作者：
Vos, S;Parry, RJ;Martin, JL
通讯作者：
Martin, JL
影响因子：
2.9
作者：
Krieger, E;Koraimann, G;Vriend, G
通讯作者：
Vriend, G