{"id":"https://openalex.org/W3107636879","doi":"https://doi.org/10.1021/acs.jcim.0c01095","title":"A Consistent Scheme for Gradient-Based Optimization of Protein<b>\u2013</b>Ligand Poses","display_name":"A Consistent Scheme for Gradient-Based Optimization of Protein<b>\u2013</b>Ligand Poses","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3107636879","doi":"https://doi.org/10.1021/acs.jcim.0c01095","mag":"3107636879","pmid":"https://pubmed.ncbi.nlm.nih.gov/33258376"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c01095","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01095","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/A5048360660","display_name":"Florian Flachsenberg","orcid":"https://orcid.org/0000-0001-7051-8719"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Florian Flachsenberg","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7051-8719","affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003179071","display_name":"Agnes Meyder","orcid":"https://orcid.org/0000-0001-8519-5780"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Agnes Meyder","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8519-5780","affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019475748","display_name":"Kai Sommer","orcid":"https://orcid.org/0000-0003-1866-8247"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kai Sommer","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1866-8247","affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045205619","display_name":"Patrick Penner","orcid":"https://orcid.org/0000-0003-4988-6183"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Penner","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4988-6183","affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9553-6531","affiliations":[{"raw_affiliation_string":"ZBH - Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstra\u03b2e 43, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083205378"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":4.2254,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.95216682,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"12","first_page":"6502","last_page":"6522"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9975000023841858,"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":0.9975000023841858,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9847000241279602,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9154999852180481,"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/broyden\u2013fletcher\u2013goldfarb\u2013shanno-algorithm","display_name":"Broyden\u2013Fletcher\u2013Goldfarb\u2013Shanno algorithm","score":0.8796429634094238},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5768564939498901},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5355017185211182},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.460421085357666},{"id":"https://openalex.org/keywords/differentiable-function","display_name":"Differentiable function","score":0.4420733153820038},{"id":"https://openalex.org/keywords/optimization-algorithm","display_name":"Optimization algorithm","score":0.4338366985321045},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4111138880252838},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3865510821342468},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38061079382896423},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2879721522331238}],"concepts":[{"id":"https://openalex.org/C132721684","wikidata":"https://www.wikidata.org/wiki/Q2877013","display_name":"Broyden\u2013Fletcher\u2013Goldfarb\u2013Shanno algorithm","level":3,"score":0.8796429634094238},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5768564939498901},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5355017185211182},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.460421085357666},{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.4420733153820038},{"id":"https://openalex.org/C2987595161","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Optimization algorithm","level":2,"score":0.4338366985321045},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4111138880252838},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3865510821342468},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38061079382896423},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2879721522331238},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C151319957","wikidata":"https://www.wikidata.org/wiki/Q752739","display_name":"Asynchronous communication","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019985","descriptor_name":"Benchmarking","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":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c01095","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c01095","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:33258376","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33258376","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":96,"referenced_works":["https://openalex.org/W436305489","https://openalex.org/W602182483","https://openalex.org/W1212579592","https://openalex.org/W1497260480","https://openalex.org/W1509196567","https://openalex.org/W1582109070","https://openalex.org/W1605578858","https://openalex.org/W1656114533","https://openalex.org/W1966490949","https://openalex.org/W1968982597","https://openalex.org/W1974977468","https://openalex.org/W1977259876","https://openalex.org/W1977467384","https://openalex.org/W1985588649","https://openalex.org/W1986476355","https://openalex.org/W1986568494","https://openalex.org/W1988437166","https://openalex.org/W1995805296","https://openalex.org/W1999329886","https://openalex.org/W2000061529","https://openalex.org/W2000359198","https://openalex.org/W2005126631","https://openalex.org/W2005136695","https://openalex.org/W2005655785","https://openalex.org/W2010099233","https://openalex.org/W2012084558","https://openalex.org/W2012231377","https://openalex.org/W2024060531","https://openalex.org/W2029087609","https://openalex.org/W2034215564","https://openalex.org/W2038210983","https://openalex.org/W2038542598","https://openalex.org/W2041902442","https://openalex.org/W2042071104","https://openalex.org/W2042572511","https://openalex.org/W2044735996","https://openalex.org/W2047730466","https://openalex.org/W2049417369","https://openalex.org/W2051434435","https://openalex.org/W2051669046","https://openalex.org/W2052789270","https://openalex.org/W2052907531","https://openalex.org/W2056641273","https://openalex.org/W2061346531","https://openalex.org/W2064747164","https://openalex.org/W2072323125","https://openalex.org/W2076961143","https://openalex.org/W2078409719","https://openalex.org/W2091917610","https://openalex.org/W2097472327","https://openalex.org/W2100598991","https://openalex.org/W2103111465","https://openalex.org/W2109364787","https://openalex.org/W2113957471","https://openalex.org/W2114779636","https://openalex.org/W2114819818","https://openalex.org/W2118512515","https://openalex.org/W2118675755","https://openalex.org/W2127790232","https://openalex.org/W2133641393","https://openalex.org/W2134967712","https://openalex.org/W2151065891","https://openalex.org/W2155384593","https://openalex.org/W2160960847","https://openalex.org/W2162166182","https://openalex.org/W2165558283","https://openalex.org/W2167577803","https://openalex.org/W2171234651","https://openalex.org/W2171242938","https://openalex.org/W2220825152","https://openalex.org/W2230466458","https://openalex.org/W2293883304","https://openalex.org/W2417863416","https://openalex.org/W2478092469","https://openalex.org/W2550887636","https://openalex.org/W2559603838","https://openalex.org/W2583907533","https://openalex.org/W2587598315","https://openalex.org/W2614021444","https://openalex.org/W2754127623","https://openalex.org/W2774371249","https://openalex.org/W2801578550","https://openalex.org/W2883886126","https://openalex.org/W2902812092","https://openalex.org/W2911847761","https://openalex.org/W2918239264","https://openalex.org/W2921473648","https://openalex.org/W2955986556","https://openalex.org/W3005417975","https://openalex.org/W3029645440","https://openalex.org/W3104705366","https://openalex.org/W3105968297","https://openalex.org/W3122563667","https://openalex.org/W3209627872","https://openalex.org/W6601260659","https://openalex.org/W6610066791"],"related_works":["https://openalex.org/W2016852760","https://openalex.org/W1972403393","https://openalex.org/W3078710903","https://openalex.org/W2787890441","https://openalex.org/W2050511877","https://openalex.org/W3114286735","https://openalex.org/W2960088919","https://openalex.org/W3128946703","https://openalex.org/W2375120501","https://openalex.org/W4311361601"],"abstract_inverted_index":{"Scoring":[0],"and":[1,26,48,71,81,156,165],"numerical":[2,36,83],"optimization":[3,37,129,157],"of":[4,11,20,54,58,107,113,118,135,149],"protein-ligand":[5],"poses":[6],"is":[7,159],"an":[8,105],"integral":[9],"part":[10],"docking":[12,98],"tools.":[13],"Although":[14],"many":[15,19],"scoring":[16,47,75,87,120,150,155],"functions":[17],"exist,":[18],"them":[21],"are":[22,28],"not":[23],"continuously":[24],"differentiable":[25],"they":[27],"rarely":[29],"explicitly":[30],"analyzed":[31],"with":[32,104,121,138],"respect":[33],"to":[34],"their":[35],"behavior.":[38],"Here,":[39],"we":[40],"present":[41],"a":[42,55,90,102,126],"consistent":[43],"scheme":[44,158],"for":[45,78,162],"pose":[46,50,79,92,103],"gradient-based":[49],"optimization.":[51],"It":[52],"consists":[53],"novel":[56],"variant":[57],"the":[59,72,96,114,122,139,145],"BFGS":[60,141],"algorithm":[61,124,142],"enabling":[62],"step-length":[63],"control,":[64],"named":[65],"LSL-BFGS":[66,123],"(limited":[67],"step":[68],"length":[69],"BFGS),":[70],"empirical":[73],"JAMDA":[74,86,119,154],"function":[76,88,151],"designed":[77],"prediction":[80,93],"good":[82],"optimizability.":[84],"The":[85,116,153],"shows":[89,125],"high":[91],"performance":[94],"in":[95,110],"CASF-2016":[97],"power":[99],"benchmark,":[100],"top-ranking":[101],"RMSD":[106],"\u22642":[108],"\u00c5":[109],"about":[111],"89%":[112],"cases.":[115],"combination":[117],"significantly":[127],"higher":[128],"locality":[130],"(i.e.,":[131],"no":[132],"excessive":[133],"movement":[134],"poses)":[136],"than":[137],"classical":[140],"while":[143],"retaining":[144],"characteristically":[146],"low":[147],"number":[148],"evaluations.":[152],"freely":[160],"available":[161],"noncommercial":[163],"use":[164],"academic":[166],"research.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-14T07:44:22.658603","created_date":"2025-10-10T00:00:00"}