Prediction of protein B-factor profiles

Yuan, Z., Bailey, T. L. and Teasdale, R. D. (2005) Prediction of protein B-factor profiles. Proteins-structure Function And Bioinformatics, 58 4: 905-912. doi:10.1002/prot.20375


Author Yuan, Z.
Bailey, T. L.
Teasdale, R. D.
Title Prediction of protein B-factor profiles
Journal name Proteins-structure Function And Bioinformatics   Check publisher's open access policy
ISSN 0887-3585
Publication date 2005-01-01
Sub-type Article (original research)
DOI 10.1002/prot.20375
Volume 58
Issue 4
Start page 905
End page 912
Total pages 8
Place of publication Hoboken
Publisher Wiley-Liss
Language eng
Subject C1
270199 Biochemistry and Cell Biology not elsewhere classified
780105 Biological sciences
Abstract The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.
Keyword B-factor
Flexibility
Support Vector Regression
Evolutionary Information
Roc Analysis
Protein Sequence
Biochemistry & Molecular Biology
Biophysics
Amino-acid-sequence
Atomic Displacement Parameters
X-ray-diffraction
Solvent Accessibility
Temperature Factors
Intrinsic Disorder
Folded Proteins
Binding-sites
Data-bank
Q-Index Code C1

 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 137 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 148 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Wed, 15 Aug 2007, 16:23:41 EST