{"id":"https://openalex.org/W2165535543","doi":"https://doi.org/10.1093/nar/gku460","title":"ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites","display_name":"ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites","publication_year":2014,"publication_date":"2014-05-26","ids":{"openalex":"https://openalex.org/W2165535543","doi":"https://doi.org/10.1093/nar/gku460","mag":"2165535543","pmid":"https://pubmed.ncbi.nlm.nih.gov/24861616"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku460","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W215/7448340/gku460.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/42/W1/W215/7448340/gku460.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007997462","display_name":"Janez Konc","orcid":"https://orcid.org/0000-0003-0160-3375"},"institutions":[{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Janez Konc","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia konc@cmm.ki.si","National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia konc@cmm.ki.si","institution_ids":["https://openalex.org/I4210152560"]},{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074495088","display_name":"Du\u0161anka Jane\u017ei\u010d","orcid":"https://orcid.org/0000-0003-4067-0116"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Du\u0161anka Jane\u017ei\u010d","raw_affiliation_strings":["University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia konc@cmm.ki.si","University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia konc@cmm.ki.si","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007997462","https://openalex.org/A5074495088"],"corresponding_institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.1473,"has_fulltext":true,"cited_by_count":71,"citation_normalized_percentile":{"value":0.97514248,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"42","issue":"W1","first_page":"W215","last_page":"W220"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9947999715805054,"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/biology","display_name":"Biology","score":0.7891645431518555},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6383026242256165},{"id":"https://openalex.org/keywords/web-site","display_name":"Web site","score":0.5358893275260925},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5267322063446045},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.46959200501441956},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.4520837366580963},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.44342318177223206},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44109997153282166},{"id":"https://openalex.org/keywords/binding-protein","display_name":"Binding protein","score":0.43993672728538513},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.43301165103912354},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.422095388174057},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3749764561653137},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.34082770347595215},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3280644714832306},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2742600739002228},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23659703135490417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23105868697166443},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.1816534698009491},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.10914185643196106},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09232008457183838}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7891645431518555},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6383026242256165},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.5358893275260925},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5267322063446045},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.46959200501441956},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4520837366580963},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.44342318177223206},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44109997153282166},{"id":"https://openalex.org/C553089730","wikidata":"https://www.wikidata.org/wiki/Q4914021","display_name":"Binding protein","level":3,"score":0.43993672728538513},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.43301165103912354},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.422095388174057},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3749764561653137},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.34082770347595215},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3280644714832306},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2742600739002228},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23659703135490417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23105868697166443},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.1816534698009491},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.10914185643196106},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09232008457183838},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gku460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku460","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W215/7448340/gku460.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:24861616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24861616","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:3176830","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4086080","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:10.1093/nar/gku460","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku460","pdf_url":"https://academic.oup.com/nar/article-pdf/42/W1/W215/7448340/gku460.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6070106675","display_name":"Multiscale modeling and simulation of soft and biological matter in and out of equilibrium","funder_award_id":"P1-0002","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"}],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"},{"id":"https://openalex.org/F4320327264","display_name":"Ministrstvo za visoko \u0161olstvo, znanost in tehnologijo","ror":"https://ror.org/0452h9305"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165535543.pdf","grobid_xml":"https://content.openalex.org/works/W2165535543.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1969001875","https://openalex.org/W1970008650","https://openalex.org/W1973462822","https://openalex.org/W1990495809","https://openalex.org/W2003402631","https://openalex.org/W2011703027","https://openalex.org/W2020383072","https://openalex.org/W2024005354","https://openalex.org/W2025536082","https://openalex.org/W2039636022","https://openalex.org/W2059446387","https://openalex.org/W2076764146","https://openalex.org/W2096863497","https://openalex.org/W2104812418","https://openalex.org/W2109464129","https://openalex.org/W2112213938","https://openalex.org/W2113494611","https://openalex.org/W2125200271","https://openalex.org/W2131085812","https://openalex.org/W2138770756","https://openalex.org/W2140538197","https://openalex.org/W2140917955","https://openalex.org/W2144477832","https://openalex.org/W2145416858","https://openalex.org/W2160642098","https://openalex.org/W2162011385","https://openalex.org/W2170441710","https://openalex.org/W2170610309","https://openalex.org/W2183091601","https://openalex.org/W4247105055","https://openalex.org/W6685863130"],"related_works":["https://openalex.org/W4281726759","https://openalex.org/W4324082543","https://openalex.org/W3144103640","https://openalex.org/W3032892710","https://openalex.org/W2892531615","https://openalex.org/W2139064989","https://openalex.org/W792740904","https://openalex.org/W2063460347","https://openalex.org/W2945199349","https://openalex.org/W2165535543"],"abstract_inverted_index":{"The":[0,72],"ProBiS-ligands":[1,20,73],"web":[2,74,81],"server":[3,50],"predicts":[4],"binding":[5,18,33,46],"of":[6,39,78],"ligands":[7],"to":[8,59,87],"a":[9,14],"protein":[10,15,42],"structure.":[11],"Starting":[12],"with":[13],"structure":[16],"or":[17],"site,":[19],"first":[21],"identifies":[22],"template":[23],"proteins":[24],"in":[25],"the":[26,37,40,44,49,53,60,79],"Protein":[27],"Data":[28],"Bank":[29],"that":[30],"share":[31],"similar":[32,45],"sites.":[34],"Based":[35],"on":[36],"superimpositions":[38],"query":[41,61],"and":[43,85],"sites":[47,58],"found,":[48],"then":[51],"transposes":[52],"ligand":[54,64],"structures":[55],"from":[56],"those":[57],"protein.":[62],"Such":[63],"prediction":[65],"supports":[66],"many":[67],"activities,":[68],"e.g.":[69],"drug":[70],"repurposing.":[71],"server,":[75,82],"an":[76],"extension":[77],"ProBiS":[80],"is":[83],"open":[84],"free":[86],"all":[88],"users":[89],"at":[90],"http://probis.cmm.ki.si/ligands.":[91]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":9},{"year":2015,"cited_by_count":5}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
