MSDmotif: exploring protein sites and motifs.
MSDmotif: exploring protein sites and motifs.
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DOI：
10.1186/1471-2105-9-312
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发表时间：
2008-07-17
影响因子：
3
通讯作者：
Henrick K
中科院分区：
文献类型：
--
作者：
Golovin A;Henrick K
蛋白质结构具有保守的特征——基序，它们对蛋白质功能有足够的影响。这些图案可以按顺序以及在 3D 空间中找到。了解这些片段对于 3D 结构预测、建模和药物设计至关重要。蛋白质数据库 (PDB) 是该信息的来源，但现有的搜索工具将蛋白质序列与其 3D 结构整合的 3D 选项有限。我们在这里描述了一个用于查询 PDB 配体、结合位点、小型 3D 结构和序列基序以及底层数据库的 Web 应用程序。纳入了化学片段、3D 基序、ψ/ψ 序列、超二级结构基序和小型 3D 结构基序关联搜索的新算法。该界面提供可视化、搜索条件创建、序列和 3D 多重对齐选项的功能。 MSDmotif 是一个集成系统，其中结果页面也是搜索表单。一组主题统计数据可用于分析。该组包括分子和基序结合统计数据、基序序列的分布、基序内氨基酸的出现、基序内氨基酸侧链电荷的相关性以及每个残基的 Ramachandran 图。结合统计数据与包括配体片段库的特性相关联。还通过分布式注释系统 (DAS) 协议提供访问。附加入口点通过 XML 响应来促进 XML 请求。 MSDmotif 的独特之处在于将化学、序列和 3D 数据结合在一个搜索引擎中，并提供一系列搜索和可视化选项。它提供了 PDB 档案中数据的多个视图，用于探索蛋白质结构。
Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB) is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS) protocol. An additional entry point facilitates XML requests with XML responses. MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
5.8
作者：
Kaur, H;Raghava, GPS
通讯作者：
Raghava, GPS
DOI：
10.1093/protein/4.3.245
发表时间：
1991-02-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
EFIMOV, AV
通讯作者：
EFIMOV, AV
影响因子：
3.5
作者：
EFIMOV, AV
通讯作者：
EFIMOV, AV
影响因子：
14.9
作者：
Hulo, N;Sigrist, CJA;Bairoch, A
通讯作者：
Bairoch, A