Naslov
DeconSTRUCT: general purpose protein database search on the substructure level

Autori
Zhang, Zong Hong ; Bharatham, Kavitha ; Sherman, Westley A. ; Mihalek, Ivana

Izvornik
Nucleic Acids Research (0305-1048) 38 (2010), Suppl_2; W590-W594

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
protein structure ; database search ; webserver

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Interdisciplinarne biotehničke znanosti, Biotehnologija u biomedicini (prirodno područje, biomedicina i zdravstvo, biotehničko područje)

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