RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes.
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes.
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DOI：
10.1093/nar/gkn197
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发表时间：
2008-07-01
影响因子：
14.9
通讯作者：
Schneider TR
中科院分区：
文献类型：
--
作者：
Mosca R;Schneider TR
蛋白质结构域快速比对（Rapido）是一个网络服务器，用于在存在构象变化的情况下对不同蛋白质分子的晶体结构进行3D比对。结构对齐算法识别在所比较的两个结构中原子间距离恒定（在定义的公差内）的等效原子组，并将这些原子组视为刚体。除了现有工具提供的功能外，RAPIDO还可以识别结构上等同的区域，当这些区域由序列上遥远且被其他可移动结构域分隔的片段组成时。此外，RAPIDO考虑到原子坐标的可靠性的变化，通过采用基于细化B值的加权函数，在比较等效原子之间的距离。通过RAPIDO鉴定为等同的区域为随后的详细分析提供了两种结构的叠加的可靠残基集。RAPIDO服务器及其相关文档可在http://webapps.embl-hamburg.de/rapido上获得。
Rapid alignment of proteins in terms of domains (RAPIDO) is a web server for the 3D alignment of crystal structures of different protein molecules in the presence of conformational change. The structural alignment algorithm identifies groups of equivalent atoms whose interatomic distances are constant (within a defined tolerance) in the two structures being compared and considers these groups of atoms as rigid bodies. In addition to the functionalities provided by existing tools, RAPIDO can identify structurally equivalent regions also when these consist of fragments that are distant in terms of sequence and separated by other movable domains. Furthermore, RAPIDO takes the variation in the reliability of atomic coordinates into account in the comparison of distances between equivalent atoms by employing weighting-functions based on the refined B-values. The regions identified as equivalent by RAPIDO furnish reliable sets of residues for the superposition of the two structures for subsequent detailed analysis. The RAPIDO server, with related documentation, is available at http://webapps.embl-hamburg.de/rapido.
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影响因子：
4
作者：
Tong, Liang;Harwood, H. James, Jr.
通讯作者：
Harwood, H. James, Jr.
影响因子：
5.7
作者：
Sierk, ML;Kleywegt, GJ
通讯作者：
Kleywegt, GJ
影响因子：
5.8
作者：
Ye, YZ;Godzik, A
通讯作者：
Godzik, A
影响因子：
2.9
作者：
Shatsky, M;Nussinov, R;Wolfson, HJ
通讯作者：
Wolfson, HJ
DOI：
10.1093/protein/11.9.739
发表时间：
1998-09-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
Shindyalov, IN;Bourne, PE
通讯作者：
Bourne, PE