{"id":"https://openalex.org/W2750193626","doi":"https://doi.org/10.1007/s10822-017-0049-y","title":"Performance of HADDOCK and a simple contact-based protein\u2013ligand binding affinity predictor in the D3R Grand Challenge 2","display_name":"Performance of HADDOCK and a simple contact-based protein\u2013ligand binding affinity predictor in the D3R Grand Challenge 2","publication_year":2017,"publication_date":"2017-08-22","ids":{"openalex":"https://openalex.org/W2750193626","doi":"https://doi.org/10.1007/s10822-017-0049-y","mag":"2750193626","pmid":"https://pubmed.ncbi.nlm.nih.gov/28831657"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-017-0049-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-017-0049-y","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs10822-017-0049-y.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007%2Fs10822-017-0049-y.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018926605","display_name":"Zeynep Kurkcuoglu","orcid":"https://orcid.org/0000-0001-7568-5882"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Zeynep Kurkcuoglu","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035389709","display_name":"Panagiotis I. Koukos","orcid":"https://orcid.org/0000-0001-6705-2815"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Panagiotis I. Koukos","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070402523","display_name":"Nevia Citro","orcid":null},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Nevia Citro","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046643239","display_name":"Mika\u00ebl Trellet","orcid":"https://orcid.org/0000-0001-6337-581X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mikael E. Trellet","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044499597","display_name":"Jo\u00e3o Rodrigues","orcid":"https://orcid.org/0000-0001-9796-3193"},"institutions":[{"id":"https://openalex.org/I130785548","display_name":"Clark University","ror":"https://ror.org/04123ky43","country_code":"US","type":"education","lineage":["https://openalex.org/I130785548"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. P. G. L. M. Rodrigues","raw_affiliation_strings":["James H. Clark Center, Stanford University, 318 Campus Drive, S210, Stanford, CA, 94305, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"James H. Clark Center, Stanford University, 318 Campus Drive, S210, Stanford, CA, 94305, USA","institution_ids":["https://openalex.org/I130785548","https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057247289","display_name":"Irina S. Moreira","orcid":"https://orcid.org/0000-0003-2970-5250"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]},{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["NL","PT"],"is_corresponding":false,"raw_author_name":"Irina S. Moreira","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","CNC - Center for Neuroscience and Cell Biology, FMUC, Universidade de Coimbra, Rua Larga, Polo I, 1\u00baandar, 3004-517, Coimbra, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"CNC - Center for Neuroscience and Cell Biology, FMUC, Universidade de Coimbra, Rua Larga, Polo I, 1\u00baandar, 3004-517, Coimbra, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086790564","display_name":"Jorge Roel\u2010Touris","orcid":"https://orcid.org/0000-0002-6588-624X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jorge Roel-Touris","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090416124","display_name":"Adrien S. J. Melquiond","orcid":"https://orcid.org/0000-0002-0167-3771"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Adrien S. J. Melquiond","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065088864","display_name":"Cunliang Geng","orcid":"https://orcid.org/0000-0002-1409-8358"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Cunliang Geng","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041551338","display_name":"J\u00f6rg Schaarschmidt","orcid":"https://orcid.org/0000-0002-4389-2366"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Schaarschmidt","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086880868","display_name":"Li C. Xue","orcid":"https://orcid.org/0000-0002-2613-538X"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Li C. Xue","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086878755","display_name":"Anna Vangone","orcid":"https://orcid.org/0000-0003-2485-7378"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Anna Vangone","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322"},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"A. M. J. J. Bonvin","raw_affiliation_strings":["Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl","Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0001-7369-1322","affiliations":[{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl","institution_ids":["https://openalex.org/I193662353"]},{"raw_affiliation_string":"Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584CH, Utrecht, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":13,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":8.1347,"has_fulltext":true,"cited_by_count":140,"citation_normalized_percentile":{"value":0.9802665,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"32","issue":"1","first_page":"175","last_page":"185"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9965000152587891,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9839000105857849,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6552690267562866},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6219127774238586},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.4692271649837494},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4232836663722992},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.41204720735549927},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3896109461784363},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.3234080672264099},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3213483393192291},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10749590396881104}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6552690267562866},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6219127774238586},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.4692271649837494},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4232836663722992},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.41204720735549927},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3896109461784363},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.3234080672264099},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3213483393192291},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10749590396881104},{"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":"D000099150","descriptor_name":"Receptor, Farnesoid X-Activated","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D011485","descriptor_name":"Protein Binding","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D018160","descriptor_name":"Receptors, Cytoplasmic and Nuclear","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","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},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1007/s10822-017-0049-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-017-0049-y","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs10822-017-0049-y.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:28831657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28831657","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5767195","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5767195","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"},{"id":"pmh:uu:oai:dspace.library.uu.nl:1874/362832","is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/362832","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Computer-Aided Molecular Design, 32(1), 175. Springer Netherlands","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s10822-017-0049-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-017-0049-y","pdf_url":"https://link.springer.com/content/pdf/10.1007%2Fs10822-017-0049-y.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.699999988079071,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G140804232","display_name":"Centre of Excellence for Biomolecular Research","funder_award_id":"675728","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1598907125","display_name":null,"funder_award_id":"INDIGO-Datacloud grant no 653549","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G1982653369","display_name":null,"funder_award_id":"675858","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G292265402","display_name":null,"funder_award_id":"675858","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2974641866","display_name":null,"funder_award_id":"653549","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G3454129258","display_name":null,"funder_award_id":"BioExcel grant no. 675728","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G4465024527","display_name":"A dynamical view of binding affinity","funder_award_id":"659025","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4562262955","display_name":"Membrane proteins \u2013 development of new computational approaches and its application to G-Protein Coupled Receptors","funder_award_id":"659826","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4562669","display_name":null,"funder_award_id":"718.015.001","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G4937468798","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5109729550","display_name":null,"funder_award_id":"722.014.005","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5317187285","display_name":null,"funder_award_id":"BAP-659025","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"},{"id":"https://openalex.org/G5411885648","display_name":null,"funder_award_id":"201406220132","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G5957263445","display_name":null,"funder_award_id":"TOP-PUNT 718.015.001","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G6029268720","display_name":null,"funder_award_id":"653549","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6355786973","display_name":null,"funder_award_id":"West-Life grant no. 675858","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G780348451","display_name":null,"funder_award_id":"MEMBRANEPROT-659826","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"},{"id":"https://openalex.org/G8167608748","display_name":null,"funder_award_id":"VENI 722.014.005","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G8875621885","display_name":null,"funder_award_id":"675728","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2750193626.pdf","grobid_xml":"https://content.openalex.org/works/W2750193626.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1030883578","https://openalex.org/W1605683241","https://openalex.org/W1653739410","https://openalex.org/W1915490970","https://openalex.org/W1948562438","https://openalex.org/W1964777932","https://openalex.org/W1977403998","https://openalex.org/W1978154436","https://openalex.org/W1979404035","https://openalex.org/W1985481261","https://openalex.org/W1998594068","https://openalex.org/W2012065014","https://openalex.org/W2018776225","https://openalex.org/W2041189078","https://openalex.org/W2045683699","https://openalex.org/W2052164601","https://openalex.org/W2071566170","https://openalex.org/W2081218071","https://openalex.org/W2099017410","https://openalex.org/W2099308584","https://openalex.org/W2105321472","https://openalex.org/W2105573149","https://openalex.org/W2114367386","https://openalex.org/W2118406741","https://openalex.org/W2122306898","https://openalex.org/W2130479394","https://openalex.org/W2134087021","https://openalex.org/W2137167381","https://openalex.org/W2138473864","https://openalex.org/W2138740386","https://openalex.org/W2139637658","https://openalex.org/W2152872596","https://openalex.org/W2153635508","https://openalex.org/W2153983456","https://openalex.org/W2154019529","https://openalex.org/W2158253179","https://openalex.org/W2165779834","https://openalex.org/W2171773193","https://openalex.org/W2204695023","https://openalex.org/W2512372054","https://openalex.org/W2548860129","https://openalex.org/W2582743722","https://openalex.org/W2587229431","https://openalex.org/W2587638657","https://openalex.org/W3128824229","https://openalex.org/W4240848616"],"related_works":["https://openalex.org/W4235673852","https://openalex.org/W4213013656","https://openalex.org/W4246463539","https://openalex.org/W1971949659","https://openalex.org/W2037320233","https://openalex.org/W2023470556","https://openalex.org/W2479478139","https://openalex.org/W2612018465","https://openalex.org/W4213356174","https://openalex.org/W4245892713"],"abstract_inverted_index":{"We":[0,145],"present":[1],"the":[2,11,15,28,36,64,76,83,95,101,105,158,168,187,202,206,214,237],"performance":[3],"of":[4,14,33,60,94,111,116,126,150,160,183,192,210,216,226],"HADDOCK,":[5],"our":[6,88,151,217],"information-driven":[7],"docking":[8,130],"software,":[9],"in":[10,48,185,222,249],"second":[12],"edition":[13],"D3R":[16],"Grand":[17],"Challenge.":[18],"In":[19],"this":[20],"blind":[21],"experiment,":[22],"participants":[23],"were":[24,70,110,118,199],"requested":[25],"to":[26,81,99,134,138,229,245],"predict":[27],"structures":[29],"and":[30,41,52,86,167],"binding":[31,142,153,175],"affinities":[32],"complexes":[34],"between":[35],"Farnesoid":[37],"X":[38],"nuclear":[39],"receptor":[40,96],"102":[42,136],"different":[43],"ligands.":[44],"The":[45,92,129],"models":[46,109],"obtained":[47,200],"Stage1":[49],"with":[50,122],"HADDOCK":[51],"ligand-specific":[53],"protocol":[54,89,131],"show":[55],"an":[56,123,223],"average":[57,124,203],"ligand":[58],"RMSD":[59,74,125],"5.1":[61],"\u00c5":[62,73],"from":[63,75,201],"crystal":[65],"structure.":[66],"Only":[67],"6/35":[68],"targets":[69],"within":[71,119,236],"2.5":[72,120,227],"reference,":[77],"which":[78],"prompted":[79],"us":[80],"investigate":[82],"limiting":[84],"factors":[85],"revise":[87],"for":[90,141,233],"Stage2.":[91],"choice":[93],"conformation":[97],"appeared":[98],"have":[100],"strongest":[102],"influence":[103],"on":[104],"results.":[106],"Our":[107],"Stage2":[108],"higher":[112],"quality":[113],"(13":[114],"out":[115,191],"35":[117],"\u00c5),":[121],"4.1":[127],"\u00c5.":[128],"was":[132],"applied":[133],"all":[135],"ligands":[137,188,235],"generate":[139],"poses":[140],"affinity":[143,154,176],"prediction.":[144],"developed":[146],"a":[147,179,230,242],"modified":[148],"version":[149],"contact-based":[152],"predictor":[155,177,232],"PRODIGY,":[156],"using":[157],"number":[159],"interatomic":[161],"contacts":[162],"classified":[163],"by":[164],"their":[165,211],"type":[166],"intermolecular":[169],"electrostatic":[170],"energy.":[171],"This":[172,220],"simple":[173,218],"structure-based":[174],"shows":[178],"Kendall's":[180],"Tau":[181],"correlation":[182],"0.37":[184],"ranking":[186,234],"(7th":[189],"best":[190],"77":[193],"methods,":[194],"5th/25":[195],"groups).":[196],"Those":[197],"results":[198,221],"prediction":[204],"over":[205],"top10":[207],"poses,":[208],"irrespective":[209],"similarity/correctness,":[212],"underscoring":[213],"robustness":[215],"predictor.":[219],"enrichment":[224],"factor":[225],"compared":[228],"random":[231],"top":[238],"25%,":[239],"making":[240],"it":[241],"promising":[243],"approach":[244],"identify":[246],"lead":[247],"compounds":[248],"virtual":[250],"screening.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":17},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
