Protemot: Prediction of protein binding sites with automatically extracted geometrical templates
Journal
Nucleic Acids Research
Journal Volume
34
Journal Issue
WEB. SERV. ISS.
Pages
W303-W309
Date Issued
2006
Author(s)
Abstract
Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein-ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries. © The Author 2006. Published by Oxford University Press. All rights reserved.
Other Subjects
access to information; article; automation; binding site; client server application; cluster analysis; complex formation; computer interface; computer prediction; computer program; controlled study; crystal structure; geometry; intermethod comparison; Internet; ligand binding; mathematical computing; priority journal; protein binding; Protein Data Bank; protein tertiary structure; response time; binding site; chemical structure; chemistry; evaluation; metabolism; protein database; structural homology; X ray crystallography; ligand; protein; Binding Sites; Crystallography, X-Ray; Databases, Protein; Internet; Ligands; Models, Molecular; Protein Structure, Tertiary; Proteins; Software; Structural Homology, Protein; User-Computer Interface
Type
journal article
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