{"id":"https://openalex.org/W4311048978","doi":"https://doi.org/10.1093/bib/bbac520","title":"A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function","display_name":"A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function","publication_year":2022,"publication_date":"2022-12-10","ids":{"openalex":"https://openalex.org/W4311048978","doi":"https://doi.org/10.1093/bib/bbac520","pmid":"https://pubmed.ncbi.nlm.nih.gov/36502369"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac520","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac520","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5101519736","display_name":"Zechen Wang","orcid":"https://orcid.org/0000-0003-4554-133X"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zechen Wang","raw_affiliation_strings":["School of Physics, Shandong University , Jinan, Shandong 250100 , China"],"raw_orcid":"https://orcid.org/0000-0003-4554-133X","affiliations":[{"raw_affiliation_string":"School of Physics, Shandong University , Jinan, Shandong 250100 , China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029472602","display_name":"Liangzhen Zheng","orcid":"https://orcid.org/0000-0003-1179-2106"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liangzhen Zheng","raw_affiliation_strings":["Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China","Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, Guangdong 518055 , China"],"raw_orcid":"https://orcid.org/0000-0003-1179-2106","affiliations":[{"raw_affiliation_string":"Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China","institution_ids":[]},{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, Guangdong 518055 , China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100371324","display_name":"Sheng Wang","orcid":"https://orcid.org/0000-0003-4210-1670"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sheng Wang","raw_affiliation_strings":["Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007757141","display_name":"Mingzhi Lin","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mingzhi Lin","raw_affiliation_strings":["Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Zelixir Biotech Company Ltd. , Shanghai 200030 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100409115","display_name":"Zhihao Wang","orcid":"https://orcid.org/0000-0001-6924-4079"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Wang","raw_affiliation_strings":["School of Physics, Shandong University , Jinan, Shandong 250100 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Shandong University , Jinan, Shandong 250100 , China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047970310","display_name":"Adams Wai\u2010Kin Kong","orcid":"https://orcid.org/0000-0002-9728-9511"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Adams Wai-Kin Kong","raw_affiliation_strings":["Rolls-Royce Corporate Lab, Nanyang Technological University , Singapore 637551 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rolls-Royce Corporate Lab, Nanyang Technological University , Singapore 637551 , Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071286986","display_name":"Yuguang Mu","orcid":"https://orcid.org/0000-0002-2499-026X"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yuguang Mu","raw_affiliation_strings":["School of Biological Sciences, Nanyang Technological University , Singapore 637551 , Singapore"],"raw_orcid":"https://orcid.org/0000-0002-2499-026X","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, Nanyang Technological University , Singapore 637551 , Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037823825","display_name":"Yanjie Wei","orcid":"https://orcid.org/0000-0002-4791-7540"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanjie Wei","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, Guangdong 518055 , China"],"raw_orcid":"https://orcid.org/0000-0002-4791-7540","affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences , Shenzhen, Guangdong 518055 , China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007365792","display_name":"Weifeng Li","orcid":"https://orcid.org/0000-0002-0244-2908"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weifeng Li","raw_affiliation_strings":["School of Physics, Shandong University , Jinan, Shandong 250100 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics, Shandong University , Jinan, Shandong 250100 , China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007365792","https://openalex.org/A5029472602"],"corresponding_institution_ids":["https://openalex.org/I154099455","https://openalex.org/I19820366","https://openalex.org/I4210145761"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.5074,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.97467583,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"1","first_page":null,"last_page":null},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9915000200271606,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9635999798774719,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.6012346148490906},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5774702429771423},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5279608964920044},{"id":"https://openalex.org/keywords/differentiable-function","display_name":"Differentiable function","score":0.5262044072151184},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.5186866521835327},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47184446454048157},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4502963721752167},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4463118314743042},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.3883149027824402},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3297204375267029},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22417554259300232},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.18220660090446472},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15399169921875},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11136621236801147},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.10933297872543335}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6012346148490906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5774702429771423},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5279608964920044},{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.5262044072151184},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.5186866521835327},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47184446454048157},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4502963721752167},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4463118314743042},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.3883149027824402},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3297204375267029},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22417554259300232},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.18220660090446472},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15399169921875},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11136621236801147},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.10933297872543335},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"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/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"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":"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:10.1093/bib/bbac520","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac520","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36502369","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36502369","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8299999833106995,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":89,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W1950993160","https://openalex.org/W1968319881","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W2001586003","https://openalex.org/W2005817231","https://openalex.org/W2009423060","https://openalex.org/W2030286884","https://openalex.org/W2042572511","https://openalex.org/W2067669378","https://openalex.org/W2101234009","https://openalex.org/W2134967712","https://openalex.org/W2148512505","https://openalex.org/W2550887636","https://openalex.org/W2578119541","https://openalex.org/W2784213390","https://openalex.org/W2807540482","https://openalex.org/W2902812092","https://openalex.org/W2921473648","https://openalex.org/W2922063386","https://openalex.org/W2943893168","https://openalex.org/W2949504121","https://openalex.org/W2951676304","https://openalex.org/W2955986556","https://openalex.org/W2969325194","https://openalex.org/W2971801381","https://openalex.org/W2972485984","https://openalex.org/W2972541552","https://openalex.org/W2974531988","https://openalex.org/W2985816842","https://openalex.org/W3004874934","https://openalex.org/W3005417975","https://openalex.org/W3008726875","https://openalex.org/W3012012790","https://openalex.org/W3020257619","https://openalex.org/W3028815767","https://openalex.org/W3030018498","https://openalex.org/W3046909847","https://openalex.org/W3048079539","https://openalex.org/W3081528324","https://openalex.org/W3087491618","https://openalex.org/W3098189759","https://openalex.org/W3118248066","https://openalex.org/W3122618795","https://openalex.org/W3128361605","https://openalex.org/W3132447912","https://openalex.org/W3135935512","https://openalex.org/W3137067752","https://openalex.org/W3138367350","https://openalex.org/W3156693194","https://openalex.org/W3157078379","https://openalex.org/W3158144848","https://openalex.org/W3162155458","https://openalex.org/W3164081635","https://openalex.org/W3165548596","https://openalex.org/W3168430821","https://openalex.org/W3172747904","https://openalex.org/W3185720802","https://openalex.org/W3194726356","https://openalex.org/W3199883166","https://openalex.org/W3207969687","https://openalex.org/W3209909976","https://openalex.org/W3215525389","https://openalex.org/W3216686093","https://openalex.org/W3217568487","https://openalex.org/W4200139236","https://openalex.org/W4210311437","https://openalex.org/W4210716706","https://openalex.org/W4213371498","https://openalex.org/W4221147818","https://openalex.org/W4224271565","https://openalex.org/W4282835253","https://openalex.org/W4289518623","https://openalex.org/W4295312788","https://openalex.org/W6640688408","https://openalex.org/W6675354045","https://openalex.org/W6765414514","https://openalex.org/W6766978945","https://openalex.org/W6776278920","https://openalex.org/W6778054072","https://openalex.org/W6782480052","https://openalex.org/W6787598838","https://openalex.org/W6796560204","https://openalex.org/W6798630201","https://openalex.org/W6802061423","https://openalex.org/W6802692787","https://openalex.org/W6803894481","https://openalex.org/W6810467923"],"related_works":["https://openalex.org/W2336040088","https://openalex.org/W2136513242","https://openalex.org/W2766845742","https://openalex.org/W2058674645","https://openalex.org/W4385073511","https://openalex.org/W1594539819","https://openalex.org/W3113038228","https://openalex.org/W3199423294","https://openalex.org/W2007257620","https://openalex.org/W2614191518"],"abstract_inverted_index":{"The":[0,83,210],"recently":[1],"reported":[2,144],"machine":[3],"learning-":[4],"or":[5],"deep":[6,207],"learning-based":[7],"scoring":[8],"functions":[9],"(SFs)":[10],"have":[11],"shown":[12],"exciting":[13],"performance":[14],"in":[15,155,171,190],"predicting":[16],"protein-ligand":[17,191],"binding":[18,35,120],"affinities":[19],"with":[20,72,98],"fruitful":[21],"application":[22],"prospects.":[23],"However,":[24],"the":[25,33,48,78,88,95,101,106,118,123,128,133,150,165,183,214],"differentiation":[26],"between":[27],"highly":[28],"similar":[29],"ligand":[30,61,119,151,203],"conformations,":[31],"including":[32],"native":[34,102],"pose":[36,62,97,103,121],"(the":[37],"global":[38],"energy":[39],"minimum":[40],"state),":[41],"remains":[42],"challenging":[43],"that":[44,179],"could":[45],"greatly":[46],"enhance":[47],"docking.":[49],"In":[50],"this":[51,169,180],"work,":[52],"we":[53],"propose":[54],"a":[55,66,73,136,199],"fully":[56,111],"differentiable,":[57],"end-to-end":[58],"framework":[59,154,170,181,216],"for":[60,201],"optimization":[63,153,215],"based":[64,205],"on":[65,206],"hybrid":[67],"SF":[68],"called":[69],"DeepRMSD+Vina":[70,134,211],"combined":[71],"multi-layer":[74],"perceptron":[75],"(DeepRMSD)":[76],"and":[77,104,161,174,213],"traditional":[79],"AutoDock":[80,107],"Vina":[81,108],"SF.":[82],"DeepRMSD+Vina,":[84],"which":[85,141],"combines":[86],"(1)":[87],"root":[89],"mean":[90],"square":[91],"deviation":[92],"(RMSD)":[93],"of":[94,116,139,168],"docking":[96,130,158],"respect":[99],"to":[100,122,146,185],"(2)":[105],"score,":[109],"is":[110,114],"differentiable;":[112],"thus":[113],"capable":[115],"optimizing":[117,202],"energy-lowest":[124],"conformation.":[125],"Evaluated":[126],"by":[127],"CASF-2016":[129],"power":[131],"dataset,":[132],"reaches":[135],"success":[137],"rate":[138],"94.4%,":[140],"outperforms":[142],"most":[143],"SFs":[145],"date.":[147],"We":[148],"evaluated":[149],"conformation":[152],"practical":[156],"molecular":[157],"scenarios":[159],"(redocking":[160],"cross-docking":[162],"tasks),":[163],"revealing":[164],"high":[166],"potentialities":[167],"drug":[172],"design":[173],"discovery.":[175],"Structural":[176],"analysis":[177],"shows":[178],"has":[182],"ability":[184],"identify":[186],"key":[187],"physical":[188],"interactions":[189],"binding,":[192],"such":[193],"as":[194],"hydrogen-bonding.":[195],"Our":[196],"work":[197],"provides":[198],"paradigm":[200],"conformations":[204],"learning":[208],"algorithms.":[209],"model":[212],"are":[217],"available":[218],"at":[219],"GitHub":[220],"repository":[221],"https://github.com/zchwang/DeepRMSD-Vina_Optimization.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":21},{"year":2023,"cited_by_count":14}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
