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Title: Alignment-free local structural search by writhe decomposition

Abstract

Motivation: Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residuelevel structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities. Results: We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizing scop domains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test. Availability: The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/

Authors:
 [1];  [2];  [2]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  2. Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1625265
Grant/Contract Number:  
AC03-76SF00098
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 26; Journal Issue: 9; Journal ID: ISSN 1367-4803
Publisher:
International Society for Computational Biology - Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Computer Science; Mathematical & Computational Biology; Mathematics

Citation Formats

Zhi, Degui, Shatsky, Maxim, and Brenner, Steven E. Alignment-free local structural search by writhe decomposition. United States: N. p., 2010. Web. doi:10.1093/bioinformatics/btq127.
Zhi, Degui, Shatsky, Maxim, & Brenner, Steven E. Alignment-free local structural search by writhe decomposition. United States. https://doi.org/10.1093/bioinformatics/btq127
Zhi, Degui, Shatsky, Maxim, and Brenner, Steven E. 2010. "Alignment-free local structural search by writhe decomposition". United States. https://doi.org/10.1093/bioinformatics/btq127. https://www.osti.gov/servlets/purl/1625265.
@article{osti_1625265,
title = {Alignment-free local structural search by writhe decomposition},
author = {Zhi, Degui and Shatsky, Maxim and Brenner, Steven E.},
abstractNote = {Motivation: Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residuelevel structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities. Results: We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizing scop domains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test. Availability: The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/},
doi = {10.1093/bioinformatics/btq127},
url = {https://www.osti.gov/biblio/1625265}, journal = {Bioinformatics},
issn = {1367-4803},
number = 9,
volume = 26,
place = {United States},
year = {2010},
month = {4}
}

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Works referencing / citing this record:

GISA: using Gauss Integrals to identify rare conformations in protein structures
journal, January 2020