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Title
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FlexPred: a web-server for predicting residue positions involved in conformational switches in proteins
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Authors
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Igor B. Kuznetsov* and Michael McDuffie
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Affiliation
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1Gen*NY*sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA
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ikuznetsov@albany.edu; Corresponding author
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+39 0825 299625
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+39 0825 299813
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Article Type
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Web Server
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Date
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received October 30, 2008; accepted November 01, 2008; published November 05, 2008
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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.
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Availability |
FlexPred is publicly available at http://flexpred.rit.albany.edu
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Keywords
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conformational variability; support vector machine; protein flexibility; structural transition; prediction | |
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Citation
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Kuznetsov & McDuffie, Bioinformation 3(3): 134-136 (2008)
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Edited by
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P. Kangueane
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ISSN
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0973-2063
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Publisher
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License
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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. |