{"id":"https://openalex.org/W2124262585","doi":"https://doi.org/10.1186/1758-2946-3-s1-p27","title":"Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections","display_name":"Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2124262585","doi":"https://doi.org/10.1186/1758-2946-3-s1-p27","mag":"2124262585"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p27","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p27","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P27","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/10.1186/1758-2946-3-S1-P27","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081139093","display_name":"Alberto Del R\u00edo","orcid":"https://orcid.org/0000-0002-1890-6797"},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"A Del Rio","raw_affiliation_strings":["Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]},{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110745143","display_name":"A.M.J.B. Barbosa","orcid":null},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"AJM Barbosa","raw_affiliation_strings":["Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]},{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025037333","display_name":"Fabiana Caporuscio","orcid":null},"institutions":[{"id":"https://openalex.org/I122346577","display_name":"University of Modena and Reggio Emilia","ror":"https://ror.org/02d4c4y02","country_code":"IT","type":"education","lineage":["https://openalex.org/I122346577"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"F Caporuscio","raw_affiliation_strings":["Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Via Campi 183, 41100, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]},{"raw_affiliation_string":"Dipartimento di Scienze Farmaceutiche, Universit\u00e0 di Modena e Reggio Emilia, Modena, Italy","institution_ids":["https://openalex.org/I122346577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081139093"],"corresponding_institution_ids":["https://openalex.org/I122346577"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.3022,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.81137636,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"S1","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":0.9998000264167786,"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":0.9998000264167786,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9889000058174133,"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":0.9869999885559082,"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/pharmacophore","display_name":"Pharmacophore","score":0.8923087120056152},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.68595951795578},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5281640887260437},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4885021448135376},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4495212435722351},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4018824100494385},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33035919070243835},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16301065683364868},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.07839429378509521}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.8923087120056152},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.68595951795578},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5281640887260437},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4885021448135376},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4495212435722351},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4018824100494385},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33035919070243835},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16301065683364868},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.07839429378509521}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-p27","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p27","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P27","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:doaj.org/article:87435f6c790b4afd8ae8ce4a8a1f832d","is_oa":true,"landing_page_url":"https://doaj.org/article/87435f6c790b4afd8ae8ce4a8a1f832d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss Suppl 1, p P27 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091962","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083582","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:10.1186/1758-2946-3-s1-p27","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p27","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P27","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2124262585.pdf","grobid_xml":"https://content.openalex.org/works/W2124262585.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W2039709045","https://openalex.org/W2043288032","https://openalex.org/W2163412990"],"related_works":["https://openalex.org/W2000397010","https://openalex.org/W2115078847","https://openalex.org/W2062768126","https://openalex.org/W2061401330","https://openalex.org/W2077097504","https://openalex.org/W2055137136","https://openalex.org/W2080809815","https://openalex.org/W2753599116","https://openalex.org/W1580389218","https://openalex.org/W2087188152"],"abstract_inverted_index":{"In":[0],"the":[1,18,35,54,74,83,92,118,129,155,161,174,178,191,269],"last":[2],"years":[3],"high-throughput":[4,122,272],"pharmacophore":[5,40,55,86,123,158,169,221,262],"screenings":[6,87,159,222],"have":[7,205],"been":[8,32],"rediscovered":[9],"as":[10],"an":[11,110,121],"effective":[12],"and":[13,63,73,243,264],"rapid":[14],"tool":[15],"for":[16,106,195,219,236],"guiding":[17],"selection":[19],"of":[20,49,71,80,95,102,132,157,163,177,211,271],"new":[21],"hit":[22],"compounds":[23,104],"with":[24,139],"predefined":[25],"biological":[26,198],"activity.":[27],"This":[28],"renaissance":[29],"has":[30],"also":[31,105],"fostered":[33],"by":[34,91,117],"current":[36],"possibility":[37,75],"to":[38,61,76,167,186,246,256],"generate":[39],"hypotheses":[41,263],"directly":[42],"from":[43],"crystallographic,":[44],"NMR":[45],"or":[46],"computational":[47],"models":[48],"protein-ligand":[50],"complexes":[51],"[1,2].":[52],"Indeed":[53],"notion":[56],"provides":[57],"a":[58,68,164,168,196,209,241,275],"powerful":[59],"way":[60,185,245],"identify":[62],"compare":[64],"structural":[65],"features":[66],"across":[67],"large":[69],"set":[70],"molecules":[72],"screen":[77],"virtually":[78],"millions":[79],"compounds.":[81,250],"At":[82],"present":[84,226],"time":[85,127],"are":[88,190],"further":[89],"stimulated":[90],"increasing":[93],"number":[94],"chemical":[96,103,230],"vendors":[97],"that":[98,120,215,232,279],"offer":[99],"their":[100],"catalogs":[101],"this":[107],"purpose.\r\n\r\nUnfortunately,":[108],"such":[109,220],"advantage":[111],"is":[112,151,171,182],"in":[113,154],"many":[114],"cases":[115,252],"blunted":[116],"fact":[119],"screening":[124],"campaign":[125],"takes":[126],"during":[128],"preparation":[130],"steps":[131],"compound":[133],"libraries,":[134],"e.g.":[135,261],"preparing":[136],"ligand":[137,165],"structures":[138],"full":[140],"hydrogen,":[141],"tautomers,":[142],"stereoisomers":[143],"and,":[144],"most":[145],"importantly,":[146],"conformers.":[147],"The":[148],"latter":[149],"point":[150],"extremely":[152],"important":[153],"context":[156],"since":[160],"matching":[162],"molecule":[166],"hypothesis":[170],"dependent":[172],"upon":[173],"molecular":[175],"conformation":[176],"ligand.":[179],"Furthermore,":[180],"there":[181],"no":[183],"specific":[184],"predict":[187],"what":[188],"conformations":[189],"biologically":[192],"active":[193,249],"ones":[194],"given":[197],"target.":[199],"To":[200],"address":[201],"these":[202,228,282],"issues":[203],"we":[204,224],"recently":[206],"introduced":[207],"CoCoCo,":[208],"suite":[210],"free":[212],"muticonformational":[213],"databases":[214],"can":[216],"be":[217,254,285],"used":[218],"[3,4].\r\n\r\nHere":[223],"will":[225,253,284],"how":[227,258],"ready-to-use":[229],"databases,":[231],"bear":[233],"multiconformational":[234],"information":[235],"each":[237],"ligand,":[238],"may":[239,267],"provide":[240],"straightforward":[242],"time-effective":[244],"select":[247],"candidate":[248],"Different":[251],"analyzed":[255],"highlight":[257],"different":[259],"factors,":[260],"conformational":[265],"states,":[266],"influence":[268],"outcome":[270],"screenings.":[273],"Finally,":[274],"proof-of-concept":[276],"experimental":[277],"study":[278],"strongly":[280],"supports":[281],"approaches":[283],"presented.":[286]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}