ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
复制标题
DOI：
10.1093/nar/gkp316
复制
发表时间：
2009-07
影响因子：
14.9
通讯作者：
Grishin NV
中科院分区：
文献类型：
--
作者：
Shi S;Chitturi B;Grishin NV
通过比较蛋白质空间结构来评估结构相似性和确定共同区域是蛋白质功能和进化研究的重要任务。有许多服务器通过重叠和坐标或接触的密切程度来比较结构和定义蛋白质之间共同的子结构。然而，对于从事结构分类的专家来说，分析结构的自然方法是寻找特定的三维基序和模式，而不是寻找两种蛋白质的共同特征。这些图案可以用主要次级结构元素（sse）的结构和拓扑来描述，而不考虑三维坐标的细微差异。尽管基于主题的结构搜索很重要，但目前执行该任务的服务器还很短缺。众所周知的TOPS并没有完全解决这个问题，因为它只找到拓扑匹配，而没有考虑其他重要的空间性质，如相互作用和手性。在这里，我们将蛋白质结构模式搜索（ProSMoS）作为web服务器来实现。ProSMoS将三维结构转换为相互作用矩阵表示，包括SSE类型、SSE之间连接的手性、SSE开始和结束的坐标、SSE之间的相互作用类型和β-sheet定义。对于用户定义的结构模式，ProSMoS列出数据库中包含此模式的所有结构。ProSMoS服务器将对结构生物学家感兴趣，他们想分析非常普遍和遥远的结构相似性。ProSMoS web服务器的网址是：http://prodata.swmed.edu/ProSMoS/。
Assessing structural similarity and defining common regions through comparison of protein spatial structures is an important task in functional and evolutionary studies of proteins. There are many servers that compare structures and define sub-structures in common between proteins through superposition and closeness of either coordinates or contacts. However, a natural way to analyze a structure for experts working on structure classification is to look for specific three-dimensional (3D) motifs and patterns instead of finding common features in two proteins. Such motifs can be described by the architecture and topology of major secondary structural elements (SSEs) without consideration of subtle differences in 3D coordinates. Despite the importance of motif-based structure searches, currently there is a shortage of servers to perform this task. Widely known TOPS does not fully address this problem, as it finds only topological match but does not take into account other important spatial properties, such as interactions and chirality. Here, we implemented our approach to protein structure pattern search (ProSMoS) as a web-server. ProSMoS converts 3D structure into an interaction matrix representation including the SSE types, handednesses of connections between SSEs, coordinates of SSE starts and ends, types of interactions between SSEs and β-sheet definitions. For a user-defined structure pattern, ProSMoS lists all structures from a database that contain this pattern. ProSMoS server will be of interest to structural biologists who would like to analyze very general and distant structural similarities. The ProSMoS web server is available at: http://prodata.swmed.edu/ProSMoS/.
登录
查看更多内容
影响因子：
2.9
作者：
Kamat, Akhil P.;Lesk, Arthur M.
通讯作者：
Lesk, Arthur M.
影响因子：
5.8
作者：
Shi, Shuoyong;Zhong, Yi;Grishin, Nick V.
通讯作者：
Grishin, Nick V.
影响因子：
1.7
作者：
Eidhammer, I;Jonassen, I;Taylor, WR
通讯作者：
Taylor, WR
影响因子：
5.8
作者：
Torrance, GM;Gilbert, DR;Westhead, DW
通讯作者：
Westhead, DW
DOI：
10.1107/s0907444904026460
发表时间：
2004-12-01
影响因子：
2.2
作者：
Krissinel, E;Henrick, K
通讯作者：
Henrick, K