Objective identification of residue ranges for the superposition of protein structures.
Objective identification of residue ranges for the superposition of protein structures.
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DOI：
10.1186/1471-2105-12-170
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发表时间：
2011-05-18
影响因子：
3
通讯作者：
Güntert P
中科院分区：
文献类型：
--
作者：
Kirchner DK;Güntert P
客观地选择氨基酸残基范围用于结构叠加的自动化对于有意义和一致的蛋白质结构分析是重要的。到目前为止，还没有广泛使用的标准来选择这些残基范围的实验确定的蛋白质结构，其中手动选择残基范围或使用次优标准仍然很常见。我们提出了一种自动化和客观的方法，用于寻找氨基酸残基范围的叠加和分析的蛋白质结构，特别是结构束产生的NMR结构计算。该方法是在一个算法，CYRANGE，产量，没有蛋白质特定的参数调整，适当的残基范围内最常见的情况下，包括低精度的结构束，多结构域蛋白质，对称多聚体，和蛋白质复合物。选择残基范围以包含蛋白质结构域的残基，其数目增加将导致RMSD值急剧上升。残基范围是通过首先基于距离方差矩阵将残基聚类到域中，然后通过逐个排除残基来细化每个域的残基的初始选择，直到RMSD值的相对减小变得不显著。空位开放的罚分有利于连续的残基范围，以获得尽可能简单但不更简单的结果。结果给出了一组37种蛋白质，并与常用的蛋白质结构验证包。我们还在蛋白质数据库中提供了6351 NMR结构的残基范围。CYRANGE方法能够自动确定各种蛋白质结构的蛋白质结构束叠加的残基范围。该方法正确识别有序区域。基于CYRANGE残基范围的全局结构叠加允许结构的清晰呈现，并且所选范围内不存在不必要的小间隙。在大多数情况下，CYRANGE的残基范围包含更少的空位，并且比其他方法覆盖更大的序列部分，而不会显著增加RMSD值。因此，CYRANGE提供了一种客观和自动的方法，用于标准化蛋白质结构叠加的残基范围的选择。
The automation of objectively selecting amino acid residue ranges for structure superpositions is important for meaningful and consistent protein structure analyses. So far there is no widely-used standard for choosing these residue ranges for experimentally determined protein structures, where the manual selection of residue ranges or the use of suboptimal criteria remain commonplace. We present an automated and objective method for finding amino acid residue ranges for the superposition and analysis of protein structures, in particular for structure bundles resulting from NMR structure calculations. The method is implemented in an algorithm, CYRANGE, that yields, without protein-specific parameter adjustment, appropriate residue ranges in most commonly occurring situations, including low-precision structure bundles, multi-domain proteins, symmetric multimers, and protein complexes. Residue ranges are chosen to comprise as many residues of a protein domain that increasing their number would lead to a steep rise in the RMSD value. Residue ranges are determined by first clustering residues into domains based on the distance variance matrix, and then refining for each domain the initial choice of residues by excluding residues one by one until the relative decrease of the RMSD value becomes insignificant. A penalty for the opening of gaps favours contiguous residue ranges in order to obtain a result that is as simple as possible, but not simpler. Results are given for a set of 37 proteins and compared with those of commonly used protein structure validation packages. We also provide residue ranges for 6351 NMR structures in the Protein Data Bank. The CYRANGE method is capable of automatically determining residue ranges for the superposition of protein structure bundles for a large variety of protein structures. The method correctly identifies ordered regions. Global structure superpositions based on the CYRANGE residue ranges allow a clear presentation of the structure, and unnecessary small gaps within the selected ranges are absent. In the majority of cases, the residue ranges from CYRANGE contain fewer gaps and cover considerably larger parts of the sequence than those from other methods without significantly increasing the RMSD values. CYRANGE thus provides an objective and automatic method for standardizing the choice of residue ranges for the superposition of protein structures.
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影响因子：
14.9
作者：
Davis IW;Leaver-Fay A;Chen VB;Block JN;Kapral GJ;Wang X;Murray LW;Arendall WB 3rd;Snoeyink J;Richardson JS;Richardson DC
通讯作者：
Richardson DC
DOI：
10.1073/pnas.251532998
发表时间：
2001-12-04
影响因子：
11.1
作者：
Horst, R;Damberger, F;Wüthrich, K
通讯作者：
Wüthrich, K
影响因子：
2.7
作者：
López-Méndez, B;Pantoja-Uceda, D;Güntert, P
通讯作者：
Güntert, P
DOI：
10.1107/s0907444994010723
发表时间：
1995-03-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
DIAMOND, R
通讯作者：
DIAMOND, R
影响因子：
5.6
作者：
Herrmann, T;Güntert, P;Wüthrich, K
通讯作者：
Wüthrich, K