Introduction

BACKGROUND: Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed method computes protein structure alignments by comparing, small substructures, called neighborhoods. Two different types of neighborhoods, sequence and structure, are defined, and two algorithms arising out of the scheme are detailed. A new method for computing equivalences having non-topological similarities from pairwise similarity score is described. A novel and fast technique for comparing sequence neighborhoods is also developed. RESULTS: The experimental results show that the current programs show better performance on Fischer and Novotny's benchmark datasets, than state of the art programs, e.g. DALI, CE and SSM. Our programs were also found to calculate correct alignments for proteins with huge amount of indels and internal repeats. Finally, the sequence neighborhood based program was used in extensive fold and non-topological similarity detection experiments. The accuracy of the fold detection experiments with the new measure of similarity was found to be similar or better than that of the standard algorithm CE. CONCLUSION: A new scheme, resulting in two algorithms, have been developed, implemented and tested. The programs developed are accessible at http://mllab.csa.iisc.ernet.in/mp2/runprog.html.

Publications

  1. Comparison of protein structures by growing neighborhood alignments.
    Cite this
    Bhattacharya S, Bhattacharyya C, Chandra NR, 2007-01-01 - BMC bioinformatics

Credits

  1. Sourangshu Bhattacharya
    Developer

  2. Chiranjib Bhattacharyya
    Developer

  3. Nagasuma R Chandra
    Investigator

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Summary
AccessionBT004023
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByNagasuma R Chandra