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Bioinformatics Advance Access published online on February 2, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl032
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 10, 2005
Revised January 27, 2006
Accepted January 28, 2006

Applications note

PROFbval: predict flexible and rigid residues in proteins

Avner Schlessinger 1 *, Guy Yachdav 2, and Burkhard Rost 2

1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA; Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St. Nicholas Ave, Rm. 804, New York, NY 10032, USA
2 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA; Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St. Nicholas Ave, Rm. 804, New York, NY 10032, USA; NorthEast Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA

* To whom correspondence should be addressed.
Avner Schlessinger, E-mail: as2067{at}columbia.edu


  Abstract

Summary: The mobility of a residue on the protein surface is closely linked to its function. The identification of extremely rigid or flexible surface residues can therefore contribute information crucial for solving the complex problem of identifying functionally important residues in proteins. Mobility is commonly measured by B-value data from high-resolution three-dimensional X-ray structures. Few methods predict B-values from sequence. Here, we present PROFbval, the first web server to predict normalized B-values from amino acid sequence. The server handles amino acid sequences (or alignments) as input and outputs normalized B-value and two-state (flexible/rigid) predictions. The server also assigns a reliability index for each prediction. For example, PROFbval correctly identifies residues in active sites on the surface of enzymes as particularly rigid.

Availability: http://www.rostlab.org/services/profbval.

Associate Editor: Dmitrij Frishman
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