一种利用氨基酸序列及其二级结构分配的蛋白质短基序搜索工具。

A protein short motif search tool using amino acid sequence and their secondary structure assignment.

作者信息

Venkataraman Arun, Chew Teong Han, Hussein Zeti Azura Mohamed, Shamsir Mohd Shahir

出版信息

Bioinformation. 2011;7(6):304-6. doi: 10.6026/007/97320630007304. Epub 2011 Nov 20.

DOI:10.6026/007/97320630007304

PMID:22355226

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3280500/

Abstract

UNLABELLED

We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools.

AVAILABILITY

The database is available for free at http://birg3.fbb.utm.my/proteinsms.

摘要

未标注

我们展示了一个网络服务器的开发，这是一种蛋白质短基序搜索工具，允许用户同时搜索蛋白质序列基序及其二级结构分配。该网络服务器能够针对来自RCSB蛋白质数据库的PDB结构数据查询非常短的基序搜索，用户可以定义序列基序中氨基酸的二级结构类型。输出利用3D可视化功能，突出显示基序在结构中和相应序列上的位置。研究人员可以轻松观察结果中多个基序的位置和构象。蛋白质短基序搜索还具有用于与其他生物信息学工具接口的应用程序编程接口（API）。