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Title

 

 

 

 

 

FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins

 

Authors

 

Igor B. Kuznetsov* and Michael McDuffie

 

Affiliation

 

 

1Gen*NY*sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA

 

Email

 

ikuznetsov@albany.edu; Corresponding author

 

Phone

+39 0825 299625

 

Fax

+39 0825 299813

 

Article Type

 

Web Server

 

Date

 

 

received October 30, 2008; accepted November 01, 2008; published November 05, 2008

 

Abstract

Conformational switches observed in the protein backbone play a key role in a variety of fundamental biological activities. This paper describes a web-server that implements a pattern recognition algorithm trained on the examples from the Database of Macromolecular Movements to predict residue positions involved in conformational switches. Prediction can be performed at an adjustable false positive rate using a user-supplied protein sequence in FASTA format or a structure in a Protein Data Bank (PDB) file. If a protein sequence is submitted, then the web-server uses sequence-derived information only (such as evolutionary conservation of residue positions). If a PDB file is submitted, then the web-server uses sequence-derived information and residue solvent accessibility calculated from this file.

 

Availability

FlexPred is publicly available at http://flexpred.rit.albany.edu

 

 

Keywords

 

 

conformational variability; support vector machine; protein flexibility; structural transition; prediction

Citation

 

Kuznetsov & McDuffie, Bioinformation 3(3): 134-136 (2008)

 

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

 

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.