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

Summary 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 (˜96%), with the correct prediction ranking first in 349 cases (˜98% of the latter, ˜94% 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. Availability and implementation LIBRA‐WA and LIBRA+ are available at: http://www.computationalbiology.it/software.html. Contact polticel@uniroma3.it Supplementary information Supplementary data are available at Bioinformatics online.

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