Campus Units

Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Baker Center for Bioinformatics and Biological Statistics

Document Type

Article

Publication Version

Published Version

Publication Date

2010

Journal or Book Title

BMC Bioinformatics

Volume

11

Issue

1

First Page

92

DOI

10.1186/1471-2105-11-92

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.

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

Copyright Owner

Feng et al

Language

en

File Format

application/pdf

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