STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
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DOI：
10.1093/nar/gkg578
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Higa, RH
中科院分区：
文献类型：
--
作者：
Neshich, G;Togawa, RC;Higa, RH
STING Millennium Suite (SMS) 是一套新的基于网络的程序和数据库套件，为蛋白质数据库 (PDB) 中存储的数据提供可视化和分子序列和结构的复杂分析。 SMS 使用公开数据（PDB、HSSP、Prosite）及其自己的数据（联系人、界面联系人、表面可访问性）的集合进行操作。生物学家发现 SMS 很有用，因为它提供了多种算法和经过验证的数据，并封装在用户友好的 Web 界面中。使用 SMS 现在可以分析序列与结构的关系、结构的质量、链内和链间类型的原子接触的性质和体积、基于多重序列比对的特定序列位置处氨基酸的相对保守性、基于残基保守性与链内接触的关系以及 Calpha-Calpha 和 Cbeta-Cbeta 距离几何关系的折叠必需残基 (FER) 的指示。 SMS 中特别强调界面形成残基 (IFR) - 定义蛋白质表面相互作用部分的氨基酸。 SMS可以同时显示和分析先前叠加的结构。 PDB 更新以同步方式触发 SMS 更新。 SMS 可在 http://www.cbi.cnptia.embrapa.br、http://mirrors.rcsb.org/SMS 和 http://trantor.bioc.columbia.edu/SMS 上免费获取公共数据。
STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). SMS operates with a collection of both publicly available data (PDB, HSSP, Prosite) and its own data (contacts, interface contacts, surface accessibility). Biologists find SMS useful because it provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. Using SMS it is now possible to analyze sequence to structure relationships, the quality of the structure, nature and volume of atomic contacts of intra and inter chain type, relative conservation of amino acids at the specific sequence position based on multiple sequence alignment, indications of folding essential residue (FER) based on the relationship of the residue conservation to the intra-chain contacts and Calpha-Calpha and Cbeta-Cbeta distance geometry. Specific emphasis in SMS is given to interface forming residues (IFR)-amino acids that define the interactive portion of the protein surfaces. SMS may simultaneously display and analyze previously superimposed structures. PDB updates trigger SMS updates in a synchronized fashion. SMS is freely accessible for public data at http://www.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS and http://trantor.bioc.columbia.edu/SMS.