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Bioinformatics Advance Access originally published online on February 2, 2006
Bioinformatics 2006 22(7):891-893; 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
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PROFbval: predict flexible and rigid residues in proteins

Avner Schlessinger 1,3,*, Guy Yachdav 1–3 and Burkhard Rost 1–3,*

1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University 650 West 168th Street BB217, New York, NY 10032, USA
2NorthEast Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University 650 West 168th Street BB217, New York, NY 10032, USA
3Columbia University Center for Computational Biology and Bioinformatics (C2B2) 1130 St Nicholas Avenue, Rm. 804, New York, NY 10032, USA

*To whom correspondence should be addressed.

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

Contact: profbval{at}rostlab.org

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on October 10, 2005; revised on January 27, 2006; accepted on January 28, 2006

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