Abstract
In the era of structural genomics, comparing a large number of protein structures can be a dauntingly time-consuming task. Traditional structural alignment methods, although offer accurate comparison, are not fast enough. Therefore, a number of databases storing pre-computed structural similarities are created to handle structural comparison queries efficiently. However, these databases cannot be updated in a timely fashion due to the sheer burden of computational requirements, thus offering only a rigid classification by some predefined parameters. Therefore, there is an increasingly urgent need for algorithms that can rapidly compare a large set of structures. Recently proposed projection methods, e.g., [1,2,3,4,5], show good promise for the development of fast structural database search solutions. Projection methods map a structure into 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. 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-based writhe decomposition protocol (inspired by [4]) that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In a benchmark test for local structural similarity detection, we show that our method, Writher, dramatically improves accuracy over current leading projection methods [4,5] in terms of recognizing SCOP domains out of multidomain proteins.
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Choi, I.G., Kwon, J., Kim, S.H.: Local feature frequency profile: A method to measure structural similarity in proteins. PNAS 101(11), 3797–3802 (2004)
Gaspari, Z., Vlahovicek, K., Pongor, S.: Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm. Bioinformatics 21(15), 3322–3323 (2005)
Lisewski, A.M., Lichtarge, O.: Rapid detection of similarity in protein structure and function through contact metric distances. Nucl. Acids Res. 34(22), e152 (2006)
Røgen, P., Fain, B.: Automatic classification of protein structure by using Gauss integrals. PNAS 100(1), 119–124 (2003)
Zotenko, E., O’Leary, D., Przytycka, T.: Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification. BMC Structural Biology 6(1), 12 (2006)
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© 2007 Springer-Verlag Berlin Heidelberg
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Zhi, D., Shatsky, M., Brenner, S.E. (2007). Alignment-Free Local Structural Search by Writhe Decomposition. In: Giancarlo, R., Hannenhalli, S. (eds) Algorithms in Bioinformatics. WABI 2007. Lecture Notes in Computer Science(), vol 4645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74126-8_18
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DOI: https://doi.org/10.1007/978-3-540-74126-8_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-74125-1
Online ISBN: 978-3-540-74126-8
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