Identification of catalytic residues from protein structure using support vector machine with sequence and structural features

Biochemical and Biophysical Research Communications
Ganesan PugalenthiRajeev Gangal

Abstract

Identification of catalytic residues can provide valuable insights into protein function. With the increasing number of protein 3D structures having been solved by X-ray crystallography and NMR techniques, it is highly desirable to develop an efficient method to identify their catalytic sites. In this paper, we present an SVM method for the identification of catalytic residues using sequence and structural features. The algorithm was applied to the 2096 catalytic residues derived from Catalytic Site Atlas database. We obtained overall prediction accuracy of 88.6% from 10-fold cross validation and 95.76% from resubstitution test. Testing on the 254 catalytic residues shows our method can correctly predict all 254 residues. This result suggests the usefulness of our approach for facilitating the identification of catalytic residues from protein structures.

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Citations

Nov 26, 2010·Journal of Computer-aided Molecular Design·Katarzyna PrymulaIrena Roterman
Apr 24, 2009·Journal of Biomolecular Structure & Dynamics·K Krishna KumarP N Suganthan
Oct 6, 2010·Journal of Biomolecular Structure & Dynamics·Ganesan PugalenthiPrasanna R Kolatkar
Jul 10, 2010·Bioinformatics·Liang-Tsung Huang, M Michael Gromiha
Jun 30, 2009·BMC Bioinformatics·Ron AlterovitzKimmen Sjölander
Aug 19, 2011·BMC Bioinformatics·Krishna Kumar KandaswamyThomas Martinetz
Jan 13, 2015·International Journal of Proteomics·Arvind Kumar Tiwari, Rajeev Srivastava
Sep 16, 2015·International Journal of Molecular Sciences·Runtao YangLina Zhang
Dec 10, 2009·Biochemical and Biophysical Research Communications·Krishna Kumar KandaswamyThomas Martinetz
Apr 28, 2009·Biochemical and Biophysical Research Communications·Ke TangSaikat Chakrabarti
Apr 15, 2011·Proteins·Ran YahalomChen Keasar
Nov 9, 2010·Journal of Theoretical Biology·Krishna Kumar KandaswamyGanesan Pugalenthi
Dec 10, 2009·PLoS Computational Biology·John A CapraThomas A Funkhouser
Nov 8, 2019·Current Pharmaceutical Design·Dan ZhangHao Lin

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