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

Date
2010-01-01
Authors
Feng, Yaping
Kloczkowski, Andrzej
Jernigan, Robert
Jernigan, Robert
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Research Projects
Organizational Units
Journal Issue
Series
Department
Biochemistry, Biophysics and Molecular BiologyBaker Center for Bioinformatics and Biological Statistics
Abstract

Background

Knowledge-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.

Results

Our 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.

Conclusions

Our 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.

Comments

This article is published as Feng, Yaping, Andrzej Kloczkowski, and Robert L. Jernigan. "Potentials' R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials." BMC bioinformatics 11, no. 1 (2010): 92. doi: 10.1186/1471-2105-11-92. Posted with permission.

Description
Keywords
Citation
DOI
Collections