{"id":"https://openalex.org/W3006485090","doi":"https://doi.org/10.1021/acs.jcim.9b01062","title":"Structural Stability Predicts the Binding Mode of Protein\u2013Ligand Complexes","display_name":"Structural Stability Predicts the Binding Mode of Protein\u2013Ligand Complexes","publication_year":2020,"publication_date":"2020-02-13","ids":{"openalex":"https://openalex.org/W3006485090","doi":"https://doi.org/10.1021/acs.jcim.9b01062","mag":"3006485090","pmid":"https://pubmed.ncbi.nlm.nih.gov/32052965"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01062","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01062","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5037500418","display_name":"Maciej Majewski","orcid":"https://orcid.org/0000-0003-2605-8166"},"institutions":[{"id":"https://openalex.org/I4388891874","display_name":"Institut de Biomedicina de la Universitat de Barcelona","ror":"https://ror.org/01y43zx14","country_code":null,"type":"education","lineage":["https://openalex.org/I4388891874","https://openalex.org/I71999127"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Maciej Majewski","raw_affiliation_strings":["Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain"],"raw_orcid":"https://orcid.org/0000-0003-2605-8166","affiliations":[{"raw_affiliation_string":"Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I4388891874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037789245","display_name":"Xavier Barril","orcid":"https://orcid.org/0000-0002-0281-1347"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I4388891874","display_name":"Institut de Biomedicina de la Universitat de Barcelona","ror":"https://ror.org/01y43zx14","country_code":null,"type":"education","lineage":["https://openalex.org/I4388891874","https://openalex.org/I71999127"]},{"id":"https://openalex.org/I71999127","display_name":"Universitat de Barcelona","ror":"https://ror.org/021018s57","country_code":"ES","type":"education","lineage":["https://openalex.org/I71999127"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Xavier Barril","raw_affiliation_strings":["Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain","Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain"],"raw_orcid":"https://orcid.org/0000-0002-0281-1347","affiliations":[{"raw_affiliation_string":"Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain","institution_ids":["https://openalex.org/I11932220"]},{"raw_affiliation_string":"Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, Barcelona 08028, Spain","institution_ids":["https://openalex.org/I71999127","https://openalex.org/I4388891874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5037789245"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I4388891874","https://openalex.org/I71999127"],"apc_list":null,"apc_paid":null,"fwci":1.8948,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.88763708,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"3","first_page":"1644","last_page":"1651"},"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":0.9991000294685364,"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/T13013","display_name":"Free Radicals and Antioxidants","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6065200567245483},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5841569900512695},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5314684510231018},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5101783275604248},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.48352670669555664},{"id":"https://openalex.org/keywords/mode","display_name":"Mode (computer interface)","score":0.4661276340484619},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4508495032787323},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4291415214538574},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3932766914367676},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.32225286960601807},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.17293351888656616},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15909156203269958},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14176863431930542},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11483699083328247},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.07710188627243042}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6065200567245483},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5841569900512695},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5314684510231018},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5101783275604248},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.48352670669555664},{"id":"https://openalex.org/C48677424","wikidata":"https://www.wikidata.org/wiki/Q6888088","display_name":"Mode (computer interface)","level":2,"score":0.4661276340484619},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4508495032787323},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4291415214538574},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3932766914367676},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.32225286960601807},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.17293351888656616},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15909156203269958},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14176863431930542},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11483699083328247},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.07710188627243042},{"id":"https://openalex.org/C185544564","wikidata":"https://www.wikidata.org/wiki/Q81197","display_name":"Nuclear physics","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b01062","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01062","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32052965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32052965","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8999999761581421}],"awards":[{"id":"https://openalex.org/G5254701857","display_name":null,"funder_award_id":"2014 SGR 1189","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G6055680192","display_name":null,"funder_award_id":"SAF2015-68749-R","funder_id":"https://openalex.org/F4320321837","funder_display_name":"Ministerio de Econom\u00eda y Competitividad"},{"id":"https://openalex.org/G796897539","display_name":"FRAGments training NETwork","funder_award_id":"675899","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"}],"funders":[{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1967348240","https://openalex.org/W1970651561","https://openalex.org/W1970658820","https://openalex.org/W1973191530","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1997305733","https://openalex.org/W1998000033","https://openalex.org/W2009529127","https://openalex.org/W2014952106","https://openalex.org/W2024704410","https://openalex.org/W2024752922","https://openalex.org/W2025970767","https://openalex.org/W2029087609","https://openalex.org/W2030980866","https://openalex.org/W2031314768","https://openalex.org/W2032617417","https://openalex.org/W2032817710","https://openalex.org/W2037535298","https://openalex.org/W2044444984","https://openalex.org/W2048214699","https://openalex.org/W2050273205","https://openalex.org/W2050456292","https://openalex.org/W2052030759","https://openalex.org/W2058835307","https://openalex.org/W2067455153","https://openalex.org/W2076419401","https://openalex.org/W2079804724","https://openalex.org/W2102377211","https://openalex.org/W2102384571","https://openalex.org/W2114779636","https://openalex.org/W2121895929","https://openalex.org/W2125782486","https://openalex.org/W2131366727","https://openalex.org/W2132629607","https://openalex.org/W2142868265","https://openalex.org/W2152964937","https://openalex.org/W2334483166","https://openalex.org/W2346117320","https://openalex.org/W2388080941","https://openalex.org/W2554932040","https://openalex.org/W2734994602","https://openalex.org/W2770371168","https://openalex.org/W2779060209","https://openalex.org/W2800745778","https://openalex.org/W2883951590","https://openalex.org/W2955254529","https://openalex.org/W2963117117","https://openalex.org/W2973686473"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"The":[0,125],"prediction":[1],"of":[2,29,72,92],"a":[3,65,128],"ligand's":[4],"binding":[5,39,46,81,120,133],"mode":[6,121,134],"into":[7],"its":[8],"macromolecular":[9],"target":[10],"is":[11,101],"essential":[12],"in":[13,64,90],"structure-based":[14],"drug":[15],"discovery.":[16],"Even":[17],"though":[18],"tremendous":[19],"effort":[20],"has":[21],"been":[22],"made":[23],"to":[24,36,53],"address":[25],"this":[26,49,55],"problem,":[27],"most":[28],"the":[30,38,70,73,84],"developed":[31],"tools":[32],"work":[33],"similarly,":[34],"trying":[35],"predict":[37],"free":[40],"energy":[41,75],"associated":[42,77],"with":[43,78,95,122,140],"each":[44,79],"particular":[45,123],"mode.":[47,82],"In":[48],"study,":[50],"we":[51],"decided":[52],"abandon":[54],"criterion,":[56],"following":[57],"structural":[58,116],"stability":[59],"instead.":[60],"This":[61],"view,":[62],"implemented":[63],"novel":[66],"computational":[67],"workflow,":[68],"quantifies":[69],"steepness":[71],"local":[74],"minimum":[76],"potential":[80],"Surprisingly,":[83],"protocol":[85],"outperforms":[86],"docking":[87,105],"scoring":[88],"functions":[89],"case":[91],"fragments":[93],"(ligands":[94],"MW":[96],"<":[97],"300":[98],"Da)":[99],"and":[100],"as":[102,104,115],"good":[103],"for":[106,132],"drug-like":[107],"molecules.":[108],"It":[109],"also":[110],"identifies":[111],"substructures":[112],"that":[113],"act":[114],"anchors,":[117],"predicting":[118],"their":[119],"accuracy.":[124],"results":[126],"open":[127],"new":[129],"physical":[130],"perspective":[131],"prediction,":[135],"which":[136],"can":[137],"be":[138],"combined":[139],"existing":[141],"thermodynamic-based":[142],"approaches.":[143]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-02T09:04:35.204637","created_date":"2025-10-10T00:00:00"}
