ArticleBioinformatics (Oxford, England)2018
LIBRA-WA: a web application for ligand binding site detection and protein function recognition.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- LVPocket: integrated 3D global-local information to protein binding pockets prediction with transfer learning of protein structure classification.Journal of cheminformatics · 2024Article
- Structure-Based Design of Small Imine Reductase Panels for Target Substrates.ACS catalysis · 2023Article
- A Guide to In Silico Drug Design.Pharmaceutics · 2022Review
- In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets.Molecules (Basel, Switzerland) · 2022Review
- FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank.Database : the journal of biological databases and curation · 2022Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina.International journal of molecular sciences · 2020Article
- Computational methods and tools for binding site recognition between proteins and small molecules: from classical geometrical approaches to modern machine learning strategies.Journal of computer-aided molecular design · 2019Article
- PrankWeb: a web server for ligand binding site prediction and visualization.Nucleic acids research · 2019Article
- Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations.International journal of molecular sciences · 2019Article
- Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.BMC bioinformatics · 2018Article
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5 authors.
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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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