Journal Article

Alignment-free local structural search by writhe decomposition

Degui Zhi, Maxim Shatsky and Steven E. Brenner

in Bioinformatics

Volume 26, issue 9, pages 1176-1184
Published in print May 2010 | ISSN: 1367-4803
Published online April 2010 | e-ISSN: 1460-2059 | DOI:

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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 residue-level 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:


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  7688 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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