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Bioinformatics. 2018 Mar 1;34(5):878-880. doi: 10.1093/bioinformatics/btx715.

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

Author information

1
Department of Sciences, University of Roma Tre, 00146 Rome, Italy.
2
Department of Science and Technology, Nguyen Tat Thanh University, Ho chi Minh City, Vietnam.
3
National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy.

Abstract

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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