{"id":"https://openalex.org/W2560290304","doi":"https://doi.org/10.1186/s13321-016-0180-0","title":"Mapping the 3D structures of small molecule binding sites","display_name":"Mapping the 3D structures of small molecule binding sites","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2560290304","doi":"https://doi.org/10.1186/s13321-016-0180-0","mag":"2560290304"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0180-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0180-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-016-0180-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-016-0180-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064142146","display_name":"Joshua Meyers","orcid":"https://orcid.org/0000-0001-5398-4355"},"institutions":[{"id":"https://openalex.org/I142947616","display_name":"Institute of Cancer Research","ror":"https://ror.org/043jzw605","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I142947616"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Joshua Meyers","raw_affiliation_strings":["Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK","institution_ids":["https://openalex.org/I142947616","https://openalex.org/I2801316944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101892657","display_name":"Nathan Brown","orcid":"https://orcid.org/0000-0001-9243-8699"},"institutions":[{"id":"https://openalex.org/I142947616","display_name":"Institute of Cancer Research","ror":"https://ror.org/043jzw605","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I142947616"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nathan Brown","raw_affiliation_strings":["Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK","institution_ids":["https://openalex.org/I142947616","https://openalex.org/I2801316944"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055979646","display_name":"Julian Blagg","orcid":"https://orcid.org/0000-0002-7409-0323"},"institutions":[{"id":"https://openalex.org/I142947616","display_name":"Institute of Cancer Research","ror":"https://ror.org/043jzw605","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I142947616"]},{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2801316944"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Julian Blagg","raw_affiliation_strings":["Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK"],"raw_orcid":"https://orcid.org/0000-0002-7409-0323","affiliations":[{"raw_affiliation_string":"Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK","institution_ids":["https://openalex.org/I142947616","https://openalex.org/I2801316944"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055979646","https://openalex.org/A5101892657"],"corresponding_institution_ids":["https://openalex.org/I142947616","https://openalex.org/I2801316944"],"apc_list":{"value":2390,"currency":"USD","value_usd":2390},"apc_paid":{"value":2390,"currency":"USD","value_usd":2390},"fwci":2.3075,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.89914147,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","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":0.9995999932289124,"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":0.9995999932289124,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9979000091552734,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9940999746322632,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.68845534324646},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6247003078460693},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.5748351216316223},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.47175198793411255},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.47108185291290283},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.44484078884124756},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.44011321663856506},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.435001015663147},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.42989328503608704},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4245948791503906},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3950120210647583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3857964873313904},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.37490761280059814},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3211613595485687},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2578727602958679},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1221112310886383}],"concepts":[{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.68845534324646},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6247003078460693},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.5748351216316223},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.47175198793411255},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.47108185291290283},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.44484078884124756},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.44011321663856506},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.435001015663147},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.42989328503608704},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4245948791503906},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3950120210647583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3857964873313904},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.37490761280059814},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3211613595485687},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2578727602958679},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1221112310886383},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/s13321-016-0180-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0180-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-016-0180-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4267511","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5395517","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-016-0180-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0180-0","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-016-0180-0","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1830539922","display_name":null,"funder_award_id":"C309/A11566","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G2448835880","display_name":"Mechanism based drug descovery.","funder_award_id":"102361","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G493830372","display_name":"Mechanism based drug descovery.","funder_award_id":"102361/Z/13/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8172221596","display_name":null,"funder_award_id":"A11566","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2560290304.pdf","grobid_xml":"https://content.openalex.org/works/W2560290304.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W567471718","https://openalex.org/W853235284","https://openalex.org/W1673310716","https://openalex.org/W1692039824","https://openalex.org/W1969370763","https://openalex.org/W1975369978","https://openalex.org/W1979414133","https://openalex.org/W1979914800","https://openalex.org/W1987847248","https://openalex.org/W1993976538","https://openalex.org/W2000077914","https://openalex.org/W2002278080","https://openalex.org/W2011301426","https://openalex.org/W2011479757","https://openalex.org/W2023004460","https://openalex.org/W2023790301","https://openalex.org/W2031168104","https://openalex.org/W2037167896","https://openalex.org/W2042110087","https://openalex.org/W2043043757","https://openalex.org/W2049663171","https://openalex.org/W2060109055","https://openalex.org/W2062051632","https://openalex.org/W2062884696","https://openalex.org/W2069344005","https://openalex.org/W2078374001","https://openalex.org/W2080653934","https://openalex.org/W2081201773","https://openalex.org/W2087179087","https://openalex.org/W2088705757","https://openalex.org/W2091708007","https://openalex.org/W2096541451","https://openalex.org/W2101234009","https://openalex.org/W2105902442","https://openalex.org/W2114162221","https://openalex.org/W2120138074","https://openalex.org/W2127067710","https://openalex.org/W2129075135","https://openalex.org/W2130479394","https://openalex.org/W2131639373","https://openalex.org/W2139362074","https://openalex.org/W2154715418","https://openalex.org/W2157825442","https://openalex.org/W2158714788","https://openalex.org/W2158804744","https://openalex.org/W2164088236","https://openalex.org/W2166410137","https://openalex.org/W2295914713","https://openalex.org/W2322633051","https://openalex.org/W2342249984","https://openalex.org/W2513297126","https://openalex.org/W2739999456","https://openalex.org/W4230466483","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4405704355","https://openalex.org/W2326230513","https://openalex.org/W4232045916","https://openalex.org/W2083843551","https://openalex.org/W4318472429","https://openalex.org/W1973079533","https://openalex.org/W2017996710","https://openalex.org/W2921492615","https://openalex.org/W2386492977","https://openalex.org/W2040535930"],"abstract_inverted_index":{"Analysis":[0],"of":[1,5,28,78,90,122,183,201,221,266],"the":[2,26,34,76,97,134,169,198,210,218,228,263],"3D":[3,264],"structures":[4,123,265],"protein\u2013ligand":[6,56,223],"binding":[7,40,45,57,93,107,116,164,181,206,224,237,268],"sites":[8,46,58,94,117,182,225],"can":[9,21,241,256],"provide":[10],"valuable":[11],"insights":[12],"for":[13,36,113,124,217],"drug":[14],"discovery.":[15],"Binding":[16],"site":[17,41,165,207,238],"comparison":[18],"(BSC)":[19],"studies":[20],"be":[22,242,257],"employed":[23],"to":[24,32,65,101,162,191,259],"elucidate":[25],"function":[27],"orphan":[29],"proteins":[30,128],"or":[31],"predict":[33],"potential":[35,55,92,115,199,222],"polypharmacology.":[37],"Many":[38],"previous":[39],"analyses":[42],"only":[43],"consider":[44],"surrounding":[47],"an":[48],"experimentally":[49],"observed":[50],"bound":[51],"ligand.":[52],"To":[53],"encompass":[54],"that":[59,235],"do":[60],"not":[61],"have":[62,68],"ligands":[63],"known":[64,190],"bind,":[66],"we":[67,86,175],"incorporated":[69],"fpocket":[70],"cavity":[71],"detection":[72,239],"software":[73],"and":[74,95,145,153,186,203],"assessed":[75],"impact":[77],"this":[79,173],"inclusion":[80],"on":[81,247],"BSC":[82,98,248],"performance.":[83,249],"Using":[84],"fpocket,":[85],"generated":[87],"a":[88,111,119,146,156,177,215],"database":[89],"ligand-independent":[91,236],"applied":[96,258],"tool,":[99],"SiteHopper,":[100],"analyze":[102],"similarity":[103],"relationships":[104,261],"between":[105,180,262],"protein":[106,131,135,188,267],"sites.":[108,269],"We":[109,158,213,233],"developed":[110],"method":[112,148],"clustering":[114,139,144],"using":[118],"curated":[120],"dataset":[121],"six":[125],"therapeutically":[126],"relevant":[127],"from":[129,155,209,227],"diverse":[130],"classes":[132],"in":[133,172],"data":[136],"bank.":[137],"Two":[138],"methods":[140],"were":[141],"explored;":[142],"hierarchical":[143],"density-based":[147],"adept":[149],"at":[150],"excluding":[151],"noise":[152],"outliers":[154],"dataset.":[157],"introduce":[159],"circular":[160],"plots":[161],"visualize":[163],"structure":[166],"space.":[167],"From":[168],"datasets":[170],"analyzed":[171],"study,":[174],"highlight":[176],"structural":[178,211,231],"relationship":[179],"cationic":[184],"trypsin":[185],"prothrombin,":[187],"targets":[189],"bind":[192],"structurally":[193],"similar":[194],"small":[195],"molecules,":[196],"exemplifying":[197],"utility":[200],"objectively":[202],"holistically":[204],"mapping":[205,220],"space":[208],"proteome.":[212,232],"present":[214],"workflow":[216],"objective":[219],"derived":[226],"currently":[229],"available":[230],"show":[234],"tools":[240,255],"introduced":[243],"without":[244],"excessive":[245],"penalty":[246],"Clustering":[250],"combined":[251],"with":[252],"intuitive":[253],"visualization":[254],"map":[260]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}