RASMOT-3D PRO: a 3D motif search webserver
RASMOT-3D PRO: a 3D motif search webserver
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DOI：
10.1093/nar/gkp304
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发表时间：
2009-07-01
影响因子：
14.9
通讯作者：
Cuniasse, Philippe
中科院分区：
文献类型：
--
作者：
Debret, Gaelle;Martel, Arnaud;Cuniasse, Philippe
蛋白质结构中残基的结构基序的检测允许鉴定蛋白质之间的结构或功能相似性。在蛋白质工程领域，结构基序鉴定对于选择蛋白质支架是必不可少的，在蛋白质支架上可以转移残基序以设计具有给定功能的新蛋白质。我们在这里描述RASMOT-3D PRO网络服务器（http：//biodev.extra.cea.fr/rasmot3d/），其在蛋白质的3D结构中执行系统搜索以寻找表现出特定拓扑结构的一组残基。比较是基于Ca和Cb原子的两个步骤：原子间距离和RMSD。RASMOT-3D PRO输入包含搜索基序的3D坐标的PDB文件，并提供显示与搜索基序相似拓扑结构残基的已鉴定蛋白质结构的交互式列表。每个解决方案都可以在网站上以图形方式进行检查。拓扑搜索可以在由用户上传的PDB文件中描述的结构中或在存放在PDB中的那些结构中进行。这一特性以及拒绝与目标空间不相容的支架的可能性，使RASMOT-3D PRO成为蛋白质工程领域的独特网络工具。
Detection of structural motif of residues in protein structures allows identification of structural or functional similarity between proteins. In the field of protein engineering, structural motif identification is essential to select protein scaffolds on which a motif of residues can be transferred to design a new protein with a given function. We describe here the RASMOT-3D PRO webserver (http://biodev.extra.cea.fr/rasmot3d/) that performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology. Comparison is based on Ca and Cb atoms in two steps: interatomic distances and RMSD. RASMOT-3D PRO takes in input a PDB file containing the 3D coordinates of the searched motif and provides an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched. Each solution can be graphically examined on the website. The topological search can be conducted in structures described in PDB files uploaded by the user or in those deposited in the PDB. This characteristic as well as the possibility to reject scaffolds sterically incompatible with the target, makes RASMOT-3D PRO a unique webtool in the field of protein engineering.