Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials

BMC Bioinformatics

Software

Yaping Feng¹  Andrzej Kloczkowski¹  Robert L Jernigan¹ 

[1] Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 50011-0320, Ames, IA, USA;LH Baker Center for Bioinformatics and Biological Statistics, Iowa State University, 50011-3020, Ames, IA, USA;

关键词: Protein Data Bank;    Protein Structure Prediction;    Fold Recognition;    Nuclear Magnetic Resonance Structure;    Protein Data Bank File;   

DOI  :  10.1186/1471-2105-11-92

 received in 2009-07-31, accepted in 2010-02-17,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundKnowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, protein design, and many other purposes. However generally these are not readily accessible online.ResultsOur new knowledge-based potential server makes available many of these potentials for easy use to automatically compute the energies of protein structures or models supplied. Our web server for protein energy estimation uses four-body potentials, short-range potentials, and 23 different two-body potentials. Users can select potentials according to their needs and preferences. Files containing the coordinates of protein atoms in the PDB format can be uploaded as input. The results will be returned to the user's email address.ConclusionsOur Potentials 'R'Us server is an easily accessible, freely available tool with a web interface that collects all existing and future protein coarse-grained potentials and computes energies of multiple structural models.

【 授权许可】

Unknown   
© Feng et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.