Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA's effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA's performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits. LIBRA-WA also sports additional functionalities like ligand clustering and a completely redesigned interface for an easier analysis of the output. Extensive tests on 373 apoprotein structures indicate that LIBRA-WA is able to identify the biologically relevant ligand/ligand binding site in 357 cases (9̃6%), with the correct prediction ranking first in 349 cases (%̃ of the latter, 9̃4% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA's improved engine for cross-compatibility purposes.

Toti, D., Le, V.H., Tortosa, V., Brandi, V., & Polticelli, F. (2018). LIBRA-WA: a web application for ligand binding site detection and protein function recognition. BIOINFORMATICS, 34(5), 878-880 [10.1093/bioinformatics/btx715].

LIBRA-WA: a web application for ligand binding site detection and protein function recognition

Toti, Daniele;Le, Viet Hung;Tortosa, Valentina;Brandi, Valentina;Polticelli, Fabio
2018

Abstract

Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA's effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA's performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits. LIBRA-WA also sports additional functionalities like ligand clustering and a completely redesigned interface for an easier analysis of the output. Extensive tests on 373 apoprotein structures indicate that LIBRA-WA is able to identify the biologically relevant ligand/ligand binding site in 357 cases (9̃6%), with the correct prediction ranking first in 349 cases (%̃ of the latter, 9̃4% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA's improved engine for cross-compatibility purposes.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11590/330747
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