Abstract
For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.
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© 2006 Springer-Verlag Berlin Heidelberg
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Huang, Z., Zhou, X., Shen, H.T., Song, D. (2006). 3D Protein Structure Matching by Patch Signatures. In: Bressan, S., Küng, J., Wagner, R. (eds) Database and Expert Systems Applications. DEXA 2006. Lecture Notes in Computer Science, vol 4080. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11827405_52
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DOI: https://doi.org/10.1007/11827405_52
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-37871-6
Online ISBN: 978-3-540-37872-3
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