{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T12:14:47Z","timestamp":1762604087035,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,11,6]],"date-time":"2017-11-06T00:00:00Z","timestamp":1509926400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Recently, LIBRA, a tool for active\/ligand binding site prediction, was described. LIBRA\u2019s 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\u2019s 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 (\u223c96%), with the correct prediction ranking first in 349 cases (\u223c98% of the latter, \u223c94% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA\u2019s improved engine for cross-compatibility purposes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>LIBRA-WA and LIBRA+ are available at: http:\/\/www.computationalbiology.it\/software.html.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx715","type":"journal-article","created":{"date-parts":[[2017,11,4]],"date-time":"2017-11-04T12:08:59Z","timestamp":1509797339000},"page":"878-880","source":"Crossref","is-referenced-by-count":25,"title":["LIBRA-WA: a web application for ligand binding site detection and protein function recognition"],"prefix":"10.1093","volume":"34","author":[{"given":"Daniele","family":"Toti","sequence":"first","affiliation":[{"name":"Department of Sciences, University of Roma Tre, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Le","family":"Viet Hung","sequence":"additional","affiliation":[{"name":"Department of Science and Technology, Nguyen Tat Thanh University, Ho chi Minh City, Vietnam"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Tortosa","sequence":"additional","affiliation":[{"name":"Department of Sciences, University of Roma Tre, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Brandi","sequence":"additional","affiliation":[{"name":"Department of Sciences, University of Roma Tre, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7657-2019","authenticated-orcid":false,"given":"Fabio","family":"Polticelli","sequence":"additional","affiliation":[{"name":"Department of Sciences, University of Roma Tre, Rome, Italy"},{"name":"National Institute of Nuclear Physics, Roma Tre Section, Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,11,6]]},"reference":[{"key":"2023012712410513500_btx715-B1","first-page":"59","article-title":"A framework for semi-automatic identification, disambiguation and storage of protein-related abbreviations in scientific literature","volume":"5767646","author":"Atzeni","year":"2011","journal-title":"Proc. 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