{"id":"https://openalex.org/W2806017263","doi":"https://doi.org/10.1515/bams-2018-0004","title":"Protein-ligand binding site detection as an alternative route to molecular docking and drug repurposing","display_name":"Protein-ligand binding site detection as an alternative route to molecular docking and drug repurposing","publication_year":2018,"publication_date":"2018-05-26","ids":{"openalex":"https://openalex.org/W2806017263","doi":"https://doi.org/10.1515/bams-2018-0004","mag":"2806017263"},"language":"en","primary_location":{"id":"doi:10.1515/bams-2018-0004","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2018-0004","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053981686","display_name":"Daniele Toti","orcid":"https://orcid.org/0000-0002-9668-6961"},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniele Toti","raw_affiliation_strings":["Department of Sciences , Roma Tre University , 00146 Rome , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Sciences , Roma Tre University , 00146 Rome , Italy","institution_ids":["https://openalex.org/I119003972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059469236","display_name":"Gabriele Macari","orcid":"https://orcid.org/0000-0001-7519-4418"},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriele Macari","raw_affiliation_strings":["Department of Sciences , Roma Tre University , 00146 Rome , Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Sciences , Roma Tre University , 00146 Rome , Italy","institution_ids":["https://openalex.org/I119003972"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079354466","display_name":"Fabio Polticelli","orcid":"https://orcid.org/0000-0002-7657-2019"},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]},{"id":"https://openalex.org/I160013858","display_name":"Istituto Nazionale di Fisica Nucleare","ror":"https://ror.org/005ta0471","country_code":"IT","type":"government","lineage":["https://openalex.org/I160013858"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Fabio Polticelli","raw_affiliation_strings":["Department of Sciences , Roma Tre University , 00146 Rome , Italy","National Institute of Nuclear Physics, Roma Tre Section , 00146 Rome , Italy"],"raw_orcid":"https://orcid.org/0000-0002-7657-2019","affiliations":[{"raw_affiliation_string":"Department of Sciences , Roma Tre University , 00146 Rome , Italy","institution_ids":["https://openalex.org/I119003972"]},{"raw_affiliation_string":"National Institute of Nuclear Physics, Roma Tre Section , 00146 Rome , Italy","institution_ids":["https://openalex.org/I160013858"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079354466"],"corresponding_institution_ids":["https://openalex.org/I119003972","https://openalex.org/I160013858"],"apc_list":null,"apc_paid":null,"fwci":0.1897,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53066104,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"14","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9901000261306763,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9718999862670898,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7695050835609436},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.764747142791748},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6705830097198486},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.655828058719635},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6519677042961121},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.611336886882782},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.607695460319519},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.6058489084243774},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.5632243156433105},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4327211081981659},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.42940646409988403},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.38210341334342957},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3349594473838806},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32181209325790405},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21181568503379822},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1660730242729187},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.15123918652534485},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.13737979531288147}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7695050835609436},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.764747142791748},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6705830097198486},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.655828058719635},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6519677042961121},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.611336886882782},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.607695460319519},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.6058489084243774},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.5632243156433105},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4327211081981659},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.42940646409988403},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.38210341334342957},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3349594473838806},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32181209325790405},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21181568503379822},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1660730242729187},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.15123918652534485},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.13737979531288147},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1515/bams-2018-0004","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2018-0004","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"},{"id":"pmh:oai:iris.uniroma3.it:11590/345566","is_oa":false,"landing_page_url":"http://hdl.handle.net/11590/345566","pdf_url":null,"source":{"id":"https://openalex.org/S4377196120","display_name":"Iris (Roma Tre University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I119003972","host_organization_name":"Roma Tre University","host_organization_lineage":["https://openalex.org/I119003972"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1994969488","https://openalex.org/W1997873916","https://openalex.org/W2018518196","https://openalex.org/W2029993405","https://openalex.org/W2047144511","https://openalex.org/W2050874067","https://openalex.org/W2052803537","https://openalex.org/W2059215264","https://openalex.org/W2072886335","https://openalex.org/W2074473216","https://openalex.org/W2090649877","https://openalex.org/W2100494857","https://openalex.org/W2105668062","https://openalex.org/W2116963147","https://openalex.org/W2120905579","https://openalex.org/W2123007244","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2140538197","https://openalex.org/W2146254854","https://openalex.org/W2154662590","https://openalex.org/W2156086712","https://openalex.org/W2157558738","https://openalex.org/W2160916724","https://openalex.org/W2176516200","https://openalex.org/W2239268835","https://openalex.org/W2266013672","https://openalex.org/W2336040088","https://openalex.org/W2375821550","https://openalex.org/W2398198205","https://openalex.org/W2415218221","https://openalex.org/W2570020953","https://openalex.org/W2570602609","https://openalex.org/W2762358889","https://openalex.org/W2767934754","https://openalex.org/W2949226104","https://openalex.org/W4245396396"],"related_works":["https://openalex.org/W2899096130","https://openalex.org/W3190782215","https://openalex.org/W2902729297","https://openalex.org/W3110500039","https://openalex.org/W4206422705","https://openalex.org/W4255531208","https://openalex.org/W4320009247","https://openalex.org/W3186872001","https://openalex.org/W3174741986","https://openalex.org/W4389861022"],"abstract_inverted_index":{"Abstract":[0],"After":[1],"the":[2,5,8,19,42,46,57,77,112,128,135,160,179,207],"onset":[3],"of":[4,10,45,61,67,131,143,164,182,184,209],"genomic":[6],"era,":[7],"detection":[9],"ligand":[11,121,144,161],"binding":[12,69,108,129,145,162,181],"sites":[13,70,109,146,151,163],"in":[14,74,86],"proteins":[15],"has":[16,49],"emerged":[17],"over":[18],"last":[20],"few":[21],"years":[22],"as":[23,89,174],"a":[24,62,125,190],"powerful":[25],"tool":[26],"for":[27,104,193],"protein":[28],"function":[29],"prediction.":[30],"Several":[31],"approaches,":[32],"both":[33],"sequence":[34],"and":[35,59,123,167,196],"structure":[36],"based,":[37],"have":[38,116,171],"been":[39,51,117,172],"developed,":[40],"but":[41],"full":[43],"potential":[44],"corresponding":[47,152],"tools":[48],"not":[50],"exploited":[52],"yet.":[53],"Here,":[54],"we":[55],"describe":[56],"development":[58],"classification":[60],"large,":[63],"almost":[64],"exhaustive,":[65],"collection":[66,142],"protein-ligand":[68],"to":[71,92,99,120,134,153,177,189,205],"be":[72,139],"used,":[73],"conjunction":[75],"with":[76],"Ligand":[78,107],"Binding":[79],"Site":[80],"Recognition":[81],"Application":[82,84],"Web":[83],"developed":[85],"our":[87],"laboratory,":[88],"an":[90],"alternative":[91],"virtual":[93],"screening":[94],"through":[95],"molecular":[96],"docking":[97],"simulations":[98],"identify":[100],"novel":[101],"lead":[102],"compounds":[103],"known":[105,126],"targets.":[106],"derived":[110],"from":[111],"Protein":[113],"Data":[114],"Bank":[115],"clustered":[118],"according":[119],"similarity,":[122],"given":[124,191],"ligand,":[127],"mode":[130],"related":[132,187],"ligands":[133],"same":[136],"target":[137,192],"can":[138],"predicted.":[140],"The":[141],"contains":[147],"more":[148,154],"than":[149,155],"200,000":[150],"20,000":[156],"different":[157],"ligands.":[158],"Furthermore,":[159],"all":[165],"Food":[166],"Drug":[168],"Administration-approved":[169],"drugs":[170],"classified":[173],"well,":[175],"allowing":[176],"investigate":[178],"possible":[180],"each":[183],"them":[185],"(and":[186],"compounds)":[188],"drug":[194],"repurposing":[195],"redesign":[197],"initiatives.":[198],"Sample":[199],"usage":[200],"cases":[201],"are":[202],"also":[203],"described":[204],"demonstrate":[206],"effectiveness":[208],"this":[210],"approach.":[211]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}