GraProStr - Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures

Q3 Computer Science

Open Bioinformatics Journal Pub Date : 2011-02-11 DOI:10.2174/1875036201105010053

M. Vijayabaskar, V. Niranjan, S. Vishveshwara

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引用次数: 20

Abstract

Protein structures can be represented as graphs/networks by defining the amino-acids as nodes and the noncovalent interactions as connections (edges). An analysis of such a graph provides valuable insights into the global structural properties, function, folding, and stability of proteins. Here we have created a webtool GraProStr to generate protein structure networks and analyze network parameters. Protein side-chain based, C /C backbone based or proteinligand Graphs/Networks can be generated using GraProStr. The well tested tool is now made available to the scientific community for the first time. GraProStr is available online and can be accessed from http://vishgraph.mbu.iisc.ernet.in/GraProStr/index.html using any of the internet browsers (best viewed in Mozilla Firefox version 3.6). The webtool is written using Perl CGI and available using Apache Webserver. With its customizable definitions of protein structure networks and well defined network parameters, GraProStr can be a very useful tool for both theoretical and experimental elucidation of protein structures.

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蛋白质结构图:一个用于构造图和生成蛋白质结构图参数的工具

通过将氨基酸定义为节点，将非共价相互作用定义为连接(边)，可以将蛋白质结构表示为图/网络。对这种图的分析提供了对蛋白质的整体结构特性、功能、折叠和稳定性的有价值的见解。在这里，我们创建了一个webtool GraProStr来生成蛋白质结构网络并分析网络参数。基于蛋白质侧链，基于C /C主链或蛋白质配体的图/网络可以使用GraProStr生成。这个经过良好测试的工具现在首次提供给科学界。GraProStr可以在线获得，可以使用任何互联网浏览器从http://vishgraph.mbu.iisc.ernet.in/GraProStr/index.html访问(最好在Mozilla Firefox 3.6版本中查看)。webtool是使用Perl CGI编写的，可以通过Apache Webserver访问。凭借其可定制的蛋白质结构网络定义和良好定义的网络参数，GraProStr可以成为蛋白质结构理论和实验阐明的非常有用的工具。

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来源期刊

Open Bioinformatics Journal Computer Science-Computer Science (miscellaneous)

CiteScore

2.40

自引率

0.00%

发文量

期刊介绍： The Open Bioinformatics Journal is an Open Access online journal, which publishes research articles, reviews/mini-reviews, letters, clinical trial studies and guest edited single topic issues in all areas of bioinformatics and computational biology. The coverage includes biomedicine, focusing on large data acquisition, analysis and curation, computational and statistical methods for the modeling and analysis of biological data, and descriptions of new algorithms and databases. The Open Bioinformatics Journal, a peer reviewed journal, is an important and reliable source of current information on the developments in the field. The emphasis will be on publishing quality articles rapidly and freely available worldwide.