article

Evaluating Protein Similarity from Coarse Structures

Authors:

Zhong-Wei Zhan,

Zhang Xiang-Sun,

Chen LuonanAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 6, Issue 4

Pages 583 - 593

https://doi.org/10.1109/TCBB.2007.70250

Published: 01 October 2009 Publication History

Abstract

To unscramble the relationship between protein function and protein structure, it is essential to assess the protein similarity from different aspects. Although many methods have been proposed for protein structure alignment or comparison, alternative similarity measures are still strongly demanded due to the requirement of fast screening and query in large-scale structure databases. In this paper, we first formulate a novel representation of a protein structure, i.e., Feature Sequence of Surface (FSS). Then, a new score scheme is developed to measure the similarity between two representations. To verify the proposed method, numerical experiments are conducted in four different protein data sets. We also classify SARS coronavirus to verify the effectiveness of the new method. Furthermore, preliminary results of fast classification of the whole CATH v2.5.1 database based on the new macrostructure similarity are given as a pilot study. We demonstrate that the proposed approach to measure the similarities between protein structures is simple to implement, computationally efficient, and surprisingly fast. In addition, the method itself provides a new and quantitative tool to view a protein structure.

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Evaluating Protein Similarity from Coarse Structures

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cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 6, Issue 4

October 2009

185 pages

ISSN:1545-5963

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IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 October 2009

Published in TCBB Volume 6, Issue 4

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Cited By

Estrada TBenson JCarrillo-Cabada HRazavi ACuendet MWeinstein HDeelman ETaufer MShehu AWu CBoucher CLi JLiu HPop M(2018)Graphic Encoding of Macromolecules for Efficient High-Throughput AnalysisProceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics10.1145/3233547.3233607(315-324)Online publication date: 15-Aug-2018
https://dl.acm.org/doi/10.1145/3233547.3233607
Gomes A(2016)A Total Order Heuristic-Based Convex Hull Algorithm for Points in the PlaneComputer-Aided Design10.1016/j.cad.2015.07.01370:C(153-160)Online publication date: 1-Jan-2016
https://dl.acm.org/doi/10.1016/j.cad.2015.07.013
Gao MCao TNanjappa ATan THuang Z(2013)gHullACM Transactions on Mathematical Software10.1145/2513109.251311240:1(1-19)Online publication date: 3-Oct-2013
https://dl.acm.org/doi/10.1145/2513109.2513112
Shibberu YHolder A(2011)A Spectral Approach to Protein Structure AlignmentIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2011.248:4(867-875)Online publication date: 1-Jul-2011
https://dl.acm.org/doi/10.1109/TCBB.2011.24

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