Protein structure search and local structure characterization.

BMC Bioinformatics
Shih-Yen Ku, Yuh-Jyh Hu

Abstract

Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D) protein structures increases, a greater variety of studies can be conducted with increasing efficiency, among which is the design of protein structural alphabets. Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D) sequence. Thus, 1D sequences can be used to identify structural similarities among proteins using standard sequence alignment tools such as BLAST or FASTA. We used self-organizing maps in combination with a minimum spanning tree algorithm to determine the optimum size of a structural alphabet and applied the k-means algorithm to group protein fragnts into clusters. The centroids of these clusters defined the structural alphabet. We also developed a flexible matrix training system to build a substitution matrix (TRISUM-169) for our alphabet. Based on FASTA and using TRISUM-169 as the substitution matrix, we developed the SA-FAST alignment tool. We compared the performance of SA-FAST with that of various search tools in database-scale search tasks...Continue Reading

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Citations

Nov 22, 2011·Computers in Biology and Medicine·Shih-Yen Ku, Yuh-Jyh Hu
Apr 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Zhiyuan ZhaiFengzhu Sun
Apr 23, 2014·Nucleic Acids Research·Eugenio MatteiManuela Helmer-Citterich
Jul 7, 2011·Biophysics Reviews·Agnel Praveen JosephAlexandre G De Brevern
May 17, 2011·Biochimie·Agnel Praveen JosephAlexandre G de Brevern
May 11, 2013·Journal of Biomolecular Structure & Dynamics·Sylvain LéonardAlexandre G de Brevern
Nov 9, 2019·Source Code for Biology and Medicine·Guilhem FaureAlexandre G de Brevern
Jan 14, 2011·Journal of Chemical Information and Modeling·Jeremy EsqueAlexandre G de Brevern

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Software Mentioned

FAST
CE
VAST
BLAST
SELECT
YAKUSA
3D
PBE
FATCAT
MEME

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