3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.
3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.
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3D-SURFER 2.0：用于实时搜索和表征蛋白质表面的网络平台。
DOI：
10.1007/978-1-4939-0366-5_8
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发表时间：
2014
期刊：
影响因子：
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通讯作者：
Kihara,Daisuke
中科院分区：
文献类型：
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作者：
Xiong,Yi;Esquivel-Rodriguez,Juan;Sael,Lee;Kihara,Daisuke
越来越多的未表征的蛋白质结构需要开发使用蛋白质三级结构进行功能注释的计算方法。蛋白质结构数据库搜索是任何基于结构的蛋白质功能阐明的基础。3D-SURFER是一个使用3D Zernike描述符对给定蛋白质结构与整个PDB进行实时蛋白质表面比较的网络平台。它可以实时地将蛋白质结构空间从一个查询结构平滑地导航到另一个查询结构。版本2.0的一个主要新功能是能够在最新的PDB中将单链、单域或单个复合体的蛋白质表面与蛋白质链、结构域、复合体或所有三者的组合的数据库进行比较。此外，现在可以比较两种类型的蛋白质结构：全原子表面和主干原子表面。服务器还可以接受用于大量数据库搜索的批处理作业。蛋白质表面的口袋可以通过VisGrid和LIGSITEcsc来识别。该服务器可在http://kiharalab.org/3d-surfer/上获得。
The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITEcsc. The server is available at http://kiharalab.org/3d-surfer/ .