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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192203/ https://www.ncbi.nlm.nih.gov/pubmed/29126218 http://dx.doi.org/10.1093/bioinformatics/btx715 |
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author | Toti, Daniele Viet Hung, Le Tortosa, Valentina Brandi, Valentina Polticelli, Fabio |
author_facet | Toti, Daniele Viet Hung, Le Tortosa, Valentina Brandi, Valentina Polticelli, Fabio |
author_sort | Toti, Daniele |
collection | PubMed |
description | 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-6192203 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-61922032019-03-01 LIBRA-WA: a web application for ligand binding site detection and protein function recognition Toti, Daniele Viet Hung, Le Tortosa, Valentina Brandi, Valentina Polticelli, Fabio Bioinformatics Applications Notes 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2018-03-01 2017-11-06 /pmc/articles/PMC6192203/ /pubmed/29126218 http://dx.doi.org/10.1093/bioinformatics/btx715 Text en © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Toti, Daniele Viet Hung, Le Tortosa, Valentina Brandi, Valentina Polticelli, Fabio LIBRA-WA: a web application for ligand binding site detection and protein function recognition |
title | LIBRA-WA: a web application for ligand binding site detection and protein
function recognition |
title_full | LIBRA-WA: a web application for ligand binding site detection and protein
function recognition |
title_fullStr | LIBRA-WA: a web application for ligand binding site detection and protein
function recognition |
title_full_unstemmed | LIBRA-WA: a web application for ligand binding site detection and protein
function recognition |
title_short | LIBRA-WA: a web application for ligand binding site detection and protein
function recognition |
title_sort | libra-wa: a web application for ligand binding site detection and protein
function recognition |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192203/ https://www.ncbi.nlm.nih.gov/pubmed/29126218 http://dx.doi.org/10.1093/bioinformatics/btx715 |
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