Terashi G, Shibuya T, Takeda-Shitaka M. LB3D: a protein three-dimensional substructure search program based on the lower bound of a root mean square deviation value.
J Comput Biol 2012;
19:493-503. [PMID:
22509779 DOI:
10.1089/cmb.2011.0230]
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Abstract
Searching for protein structure-function relationships using three-dimensional (3D) structural coordinates represents a fundamental approach for determining the function of proteins with unknown functions. Since protein structure databases are rapidly growing in size, the development of a fast search method to find similar protein substructures by comparison of protein 3D structures is essential. In this article, we present a novel protein 3D structure search method to find all substructures with root mean square deviations (RMSDs) to the query structure that are lower than a given threshold value. Our new algorithm runs in O(m + N/m(0.5)) time, after O(N log N) preprocessing, where N is the database size and m is the query length. The new method is 1.8-41.6 times faster than the practically best known O(N) algorithm, according to computational experiments using a huge database (i.e., >20,000,000 C-alpha coordinates).
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