Paper Info
Title
deconSTRUCT: general purpose protein database search on the substructure level.
Abstract
deconSTRUCT webserver offers an interface to a protein database search engine, usable for a general purpose detection of similar protein (sub) structures. Initially, it deconstructs the query structure into its secondary structure elements (SSEs) and reassembles the match to the target by requiring a (tunable) degree of similarity in the direction and sequential order of SSEs. Hierarchical organization and judicious use of the information about protein structure enables deconSTRUCT to achieve the sensitivity and specificity of the established search engines at orders of magnitude increased speed, without tying up irretrievably the substructure information in the form of a hash. In a post-processing step, a match on the level of the backbone atoms is constructed. The results presented to the user consist of the list of the matched SSEs, the transformation matrix for rigid superposition of the structures and several ways of visualization, both downloadable and implemented as a web-browser plug-in. The server is available at http://epsf.bmad.bii.a-star.edu.sg/struct_server.html.
Year
DOI
Venue
2010
10.1093/nar/gkq489
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
internet,database search,algorithms
USable,Protein structure database,Search engine,Information retrieval,Biology,Visualization,Database search engine,Hash function,Bioinformatics,Genetics,Web server,Hierarchical organization
Journal
Volume
Issue
ISSN
38
SUPnan
0305-1048
Citations 
PageRank 
References 
3
0.41
15
Authors
4
Name
Order
Citations
PageRank
Zong Hong Zhang1211.86
Kavitha Bharatham271.56
Westley A Sherman381.03
Ivana Mihalek4152.17