{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T10:59:58Z","timestamp":1768474798879,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,1,21]],"date-time":"2020-01-21T00:00:00Z","timestamp":1579564800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fundaci\u00f3n S\u00e9neca del Centro de Coordinaci\u00f3n de la Investigaci\u00f3n de la Regi\u00f3n de Murcia","award":["20813\/PI\/18"],"award-info":[{"award-number":["20813\/PI\/18"]}]},{"name":"Fundaci\u00f3n S\u00e9neca del Centro de Coordinaci\u00f3n de la Investigaci\u00f3n de la Regi\u00f3n de Murcia","award":["20988\/PI\/18"],"award-info":[{"award-number":["20988\/PI\/18"]}]},{"name":"Fundaci\u00f3n S\u00e9neca del Centro de Coordinaci\u00f3n de la Investigaci\u00f3n de la Regi\u00f3n de Murcia","award":["20524\/PDC\/18"],"award-info":[{"award-number":["20524\/PDC\/18"]}]},{"name":"Spanish Ministry of Science, Innovation and Universities","award":["TIN2016-78799-P"],"award-info":[{"award-number":["TIN2016-78799-P"]}]},{"name":"Spanish Ministry of Science, Innovation and Universities","award":["CTQ2017-87974-R"],"award-info":[{"award-number":["CTQ2017-87974-R"]}]},{"DOI":"10.13039\/501100006433","name":"Barcelona Supercomputing Center - Centro Nacional de Supercomputaci\u00f3n","doi-asserted-by":"publisher","award":["RES-BCV-2018-3-0008"],"award-info":[{"award-number":["RES-BCV-2018-3-0008"]}],"id":[{"id":"10.13039\/501100006433","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Molecular docking methods are extensively used to predict the interaction between protein\u2013ligand systems in terms of structure and binding affinity, through the optimization of a physics-based scoring function. However, the computational requirements of these simulations grow exponentially with: (i) the global optimization procedure, (ii) the number and degrees of freedom of molecular conformations generated and (iii) the mathematical complexity of the scoring function.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we introduce a novel molecular docking method named METADOCK 2, which incorporates several novel features, such as (i) a ligand-dependent blind docking approach that exhaustively scans the whole protein surface to detect novel allosteric sites, (ii) an optimization method to enable the use of a wide branch of metaheuristics and (iii) a heterogeneous implementation based on multicore CPUs and multiple graphics processing units. Two representative scoring functions implemented in METADOCK 2 are extensively evaluated in terms of computational performance and accuracy using several benchmarks (such as the well-known DUD) against AutoDock 4.2 and AutoDock Vina. Results place METADOCK 2 as an efficient and accurate docking methodology able to deal with complex systems where computational demands are staggering and which outperforms both AutoDock Vina and AutoDock 4.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/Baldoimbernon@bitbucket.org\/Baldoimbernon\/metadock_2.git.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz958","type":"journal-article","created":{"date-parts":[[2020,1,16]],"date-time":"2020-01-16T20:10:24Z","timestamp":1579205424000},"page":"1515-1520","source":"Crossref","is-referenced-by-count":15,"title":["METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking"],"prefix":"10.1093","volume":"37","author":[{"given":"Baldomero","family":"Imbern\u00f3n","sequence":"first","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]},{"given":"Antonio","family":"Serrano","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1734-6852","authenticated-orcid":false,"given":"Andr\u00e9s","family":"Bueno-Crespo","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]},{"given":"Jos\u00e9 L","family":"Abell\u00e1n","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]},{"given":"Horacio","family":"P\u00e9rez-S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]},{"given":"Jos\u00e9 M","family":"Cecilia","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Computer Engineering Department, Universidad Cat\u00f3lica de Murcia (UCAM), 30107 Murcia, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,1,21]]},"reference":[{"key":"2023051709445097500_btz958-B1","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1007\/s11047-008-9098-4","article-title":"A survey on metaheuristics for stochastic combinatorial optimization","volume":"8","author":"Bianchi","year":"2009","journal-title":"Nat. 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