{"id":"https://openalex.org/W1892290673","doi":"https://doi.org/10.1186/s13321-015-0096-0","title":"Modeling enzyme-ligand binding in drug discovery","display_name":"Modeling enzyme-ligand binding in drug discovery","publication_year":2015,"publication_date":"2015-10-06","ids":{"openalex":"https://openalex.org/W1892290673","doi":"https://doi.org/10.1186/s13321-015-0096-0","mag":"1892290673","pmid":"https://pubmed.ncbi.nlm.nih.gov/26457119"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-015-0096-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-015-0096-0","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-015-0096-0","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-015-0096-0","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/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"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":false,"raw_author_name":"Janez Konc","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia ; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000, Koper, Slovenia","National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia ; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"]},{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032088268","display_name":"Samo Le\u0161nik","orcid":"https://orcid.org/0000-0002-0613-6959"},"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":false,"raw_author_name":"Samo Le\u0161nik","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia","National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia","institution_ids":["https://openalex.org/I4210152560"]},{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-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":["Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000, Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]},{"raw_affiliation_string":"Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000, Koper, Slovenia","institution_ids":["https://openalex.org/I118905719"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074495088"],"corresponding_institution_ids":["https://openalex.org/I118905719"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":3.0084,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.91384002,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":"1","first_page":"48","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9984999895095825,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.8052718639373779},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6917892098426819},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5793755054473877},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5678554177284241},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.469830721616745},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4486449360847473},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.41566580533981323},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.4084339141845703},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3159785270690918},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3013759255409241},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25441256165504456},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21700838208198547},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.16329485177993774},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.08935487270355225}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.8052718639373779},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6917892098426819},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5793755054473877},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5678554177284241},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.469830721616745},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4486449360847473},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.41566580533981323},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4084339141845703},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3159785270690918},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3013759255409241},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25441256165504456},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21700838208198547},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.16329485177993774},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.08935487270355225},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13321-015-0096-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-015-0096-0","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-015-0096-0","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":"pmid:26457119","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26457119","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3575811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4594084","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/s13321-015-0096-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-015-0096-0","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-015-0096-0","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/G5841956236","display_name":"Razvoj ra\u010dunalni\u0161kih orodij za modeliranje farmacevtsko zanimivih molekul (Slovene)","funder_award_id":"J1-6743","funder_id":"https://openalex.org/F4320322554","funder_display_name":"Javna Agencija za Raziskovalno Dejavnost RS"},{"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"},{"id":"https://openalex.org/G8761850079","display_name":"Boj proti bakterijski rezistenci: optimizacija zaviralcev biosinteze bakterijske stene (Slovene)","funder_award_id":"L1-6745","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1892290673.pdf","grobid_xml":"https://content.openalex.org/works/W1892290673.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1969001875","https://openalex.org/W1971618381","https://openalex.org/W1985270532","https://openalex.org/W1986046522","https://openalex.org/W1990495809","https://openalex.org/W1998222399","https://openalex.org/W1998848097","https://openalex.org/W1998912666","https://openalex.org/W2005445463","https://openalex.org/W2013433800","https://openalex.org/W2015147525","https://openalex.org/W2015214828","https://openalex.org/W2015613785","https://openalex.org/W2019701333","https://openalex.org/W2020383072","https://openalex.org/W2024005354","https://openalex.org/W2025536082","https://openalex.org/W2027482274","https://openalex.org/W2039636022","https://openalex.org/W2046258407","https://openalex.org/W2047710091","https://openalex.org/W2051783184","https://openalex.org/W2053174787","https://openalex.org/W2053658804","https://openalex.org/W2055410316","https://openalex.org/W2056951033","https://openalex.org/W2059215264","https://openalex.org/W2059457452","https://openalex.org/W2061583504","https://openalex.org/W2073104301","https://openalex.org/W2075260011","https://openalex.org/W2085168902","https://openalex.org/W2089656772","https://openalex.org/W2090649877","https://openalex.org/W2096541451","https://openalex.org/W2101557653","https://openalex.org/W2103540182","https://openalex.org/W2110397834","https://openalex.org/W2112213938","https://openalex.org/W2117486996","https://openalex.org/W2121201922","https://openalex.org/W2121790192","https://openalex.org/W2125200271","https://openalex.org/W2127760066","https://openalex.org/W2128402268","https://openalex.org/W2132262459","https://openalex.org/W2134881479","https://openalex.org/W2134967712","https://openalex.org/W2138770756","https://openalex.org/W2139064989","https://openalex.org/W2140538197","https://openalex.org/W2144477832","https://openalex.org/W2145268834","https://openalex.org/W2150444353","https://openalex.org/W2158964183","https://openalex.org/W2165535543","https://openalex.org/W2166103367","https://openalex.org/W2169815691","https://openalex.org/W2170146596","https://openalex.org/W2170441710","https://openalex.org/W2183091601","https://openalex.org/W2339723380"],"related_works":["https://openalex.org/W2480711475","https://openalex.org/W4206379684","https://openalex.org/W2061997414","https://openalex.org/W1587522533","https://openalex.org/W2366105490","https://openalex.org/W2153190755","https://openalex.org/W2580680567","https://openalex.org/W2355466661","https://openalex.org/W2803627340","https://openalex.org/W2121182182"],"abstract_inverted_index":{"Enzymes":[0],"are":[1],"one":[2],"of":[3,8,17,40,61,67],"the":[4,34,37,59,65],"most":[5],"important":[6],"groups":[7],"drug":[9,22,62],"targets,":[10],"and":[11,42,51,77],"identifying":[12],"possible":[13],"ligand-enzyme":[14,44],"interactions":[15,50],"is":[16],"major":[18],"importance":[19],"in":[20,58],"many":[21],"discovery":[23,63],"processes.":[24],"Novel":[25],"computational":[26],"methods":[27],"have":[28],"been":[29],"developed":[30],"that":[31],"can":[32],"apply":[33],"information":[35],"from":[36],"increasing":[38],"number":[39],"resolved":[41],"available":[43],"complexes":[45],"to":[46,54],"model":[47],"new":[48],"unknown":[49,68],"therefore":[52],"contribute":[53],"answer":[55],"open":[56],"questions":[57],"field":[60],"like":[64],"identification":[66],"protein":[69],"functions,":[70],"off-target":[71],"binding,":[72],"ligand":[73],"3D":[74],"homology":[75],"modeling":[76],"induced-fit":[78],"simulations.":[79]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
