{"id":"https://openalex.org/W4417004357","doi":"https://doi.org/10.1186/s13321-026-01168-8","title":"Molecular embedding-based algorithm selection in protein-ligand docking","display_name":"Molecular embedding-based algorithm selection in protein-ligand docking","publication_year":2026,"publication_date":"2026-03-14","ids":{"openalex":"https://openalex.org/W4417004357","doi":"https://doi.org/10.1186/s13321-026-01168-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/41832536"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-026-01168-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01168-8","pdf_url":null,"source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13321-026-01168-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jiabao Brad Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159968","display_name":"Duke Kunshan University","ror":"https://ror.org/04sr5ys16","country_code":"CN","type":"education","lineage":["https://openalex.org/I170897317","https://openalex.org/I37461747","https://openalex.org/I4210159968"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiabao Brad Wang","raw_affiliation_strings":["Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China","institution_ids":["https://openalex.org/I4210159968"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101398440","display_name":"Siyuan Cao","orcid":"https://orcid.org/0000-0001-6947-6793"},"institutions":[{"id":"https://openalex.org/I4210159968","display_name":"Duke Kunshan University","ror":"https://ror.org/04sr5ys16","country_code":"CN","type":"education","lineage":["https://openalex.org/I170897317","https://openalex.org/I37461747","https://openalex.org/I4210159968"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Siyuan Cao","raw_affiliation_strings":["Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China","institution_ids":["https://openalex.org/I4210159968"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017997914","display_name":"Hongxuan Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159968","display_name":"Duke Kunshan University","ror":"https://ror.org/04sr5ys16","country_code":"CN","type":"education","lineage":["https://openalex.org/I170897317","https://openalex.org/I37461747","https://openalex.org/I4210159968"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongxuan Wu","raw_affiliation_strings":["Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China","institution_ids":["https://openalex.org/I4210159968"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yiliang Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Yiliang Yuan","raw_affiliation_strings":["Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence, Building 1B, Masdar City, Abu Dhabi, UAE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, Mohamed bin Zayed University of Artificial Intelligence, Building 1B, Masdar City, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024551178","display_name":"Mustafa M\u0131s\u0131r","orcid":"https://orcid.org/0000-0002-6885-6775"},"institutions":[{"id":"https://openalex.org/I4210159968","display_name":"Duke Kunshan University","ror":"https://ror.org/04sr5ys16","country_code":"CN","type":"education","lineage":["https://openalex.org/I170897317","https://openalex.org/I37461747","https://openalex.org/I4210159968"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mustafa M\u0131s\u0131r","raw_affiliation_strings":["Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China. mustafa.misir@dukekunshan.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Natural and Applied Sciences, Duke Kunshan University, 8 Duke Av., Suzhou, 215316, Jiangsu, China. mustafa.misir@dukekunshan.edu.cn","institution_ids":["https://openalex.org/I4210159968"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017997914","https://openalex.org/A5024551178","https://openalex.org/A5101398440"],"corresponding_institution_ids":["https://openalex.org/I4210113480","https://openalex.org/I4210159968"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":15.9938,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.98056426,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"18","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":0.5740000009536743,"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":0.5740000009536743,"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":0.23720000684261322,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.05119999870657921,"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/solver","display_name":"Solver","score":0.7831000089645386},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5318999886512756},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5277000069618225},{"id":"https://openalex.org/keywords/oracle","display_name":"Oracle","score":0.5008000135421753},{"id":"https://openalex.org/keywords/separable-space","display_name":"Separable space","score":0.4796999990940094}],"concepts":[{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.7831000089645386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6639999747276306},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5318999886512756},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5277000069618225},{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.5008000135421753},{"id":"https://openalex.org/C70710897","wikidata":"https://www.wikidata.org/wiki/Q680081","display_name":"Separable space","level":2,"score":0.4796999990940094},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43290001153945923},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.4307999908924103},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41819998621940613},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.39239999651908875},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.3422999978065491}],"mesh":[],"locations_count":9,"locations":[{"id":"doi:10.1186/s13321-026-01168-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01168-8","pdf_url":null,"source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:41832536","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41832536","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2512.02328","is_oa":true,"landing_page_url":"https://arxiv.org/abs/2512.02328","pdf_url":"https://arxiv.org/pdf/2512.02328","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:arXiv.org:2512.02328","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2512.02328","pdf_url":"https://arxiv.org/pdf/2512.02328","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:52b3d25513dc4cf4b6c122384344bd21","is_oa":true,"landing_page_url":"https://doaj.org/article/52b3d25513dc4cf4b6c122384344bd21","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 18, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13104262","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13104262/","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 Cheminform","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2512.02328","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2512.02328","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.6084/m9.figshare.c.8437735","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.8437735","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Collection"},{"id":"doi:10.6084/m9.figshare.c.8437735.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.8437735.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Collection"}],"best_oa_location":{"id":"doi:10.1186/s13321-026-01168-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01168-8","pdf_url":null,"source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W2943893168","https://openalex.org/W2768092025","https://openalex.org/W2028629022","https://openalex.org/W2134967712","https://openalex.org/W2148512505","https://openalex.org/W2076022099","https://openalex.org/W2152630148","https://openalex.org/W2902812092","https://openalex.org/W4404764874","https://openalex.org/W2151554678","https://openalex.org/W4407601569","https://openalex.org/W2898873842","https://openalex.org/W2102539288","https://openalex.org/W2755098789","https://openalex.org/W4377293862","https://openalex.org/W2563364594","https://openalex.org/W4412500952","https://openalex.org/W7135377966","https://openalex.org/W4411009334","https://openalex.org/W3168430821","https://openalex.org/W4414408310","https://openalex.org/W4386976834","https://openalex.org/W2587598315","https://openalex.org/W2146465875","https://openalex.org/W4389696354","https://openalex.org/W1983194490","https://openalex.org/W3082411326","https://openalex.org/W3004591935","https://openalex.org/W7090928830","https://openalex.org/W4388820090","https://openalex.org/W2918239264","https://openalex.org/W4391896776","https://openalex.org/W4408061231"],"related_works":[],"abstract_inverted_index":{"Selecting":[0],"an":[1,153,220],"effective":[2,96],"docking":[3,79,167,226,241],"algorithm":[4,168,227],"is":[5,21,94,135,170,229],"highly":[6],"context-dependent,":[7],"and":[8,17,33,39,67,87,106,121,144,159,194,200,206,215,258],"no":[9],"single":[10,63,250],"method":[11],"performs":[12],"reliably":[13],"across":[14,77],"structural,":[15],"chemical,":[16],"protocol":[18,115,256],"regimes.":[19],"MolAS":[20,52,93,151,174],"a":[22,40,47,56,107,161,176,188,249,263],"lightweight":[23],"algorithm-selection":[24],"model":[25],"that":[26,92,117,180,244],"predicts":[27],"per-algorithm":[28],"performance":[29],"from":[30,239],"pretrained":[31],"protein":[32],"ligand":[34],"embeddings":[35],"using":[36],"attentional":[37],"pooling":[38],"shallow":[41],"residual":[42],"decoder.":[43],"With":[44],"hundreds":[45],"to":[46,55,208,231,265],"few":[48],"thousand":[49],"labelled":[50],"complexes,":[51],"achieves":[53],"up":[54],"15":[57],"percentage-point":[58],"absolute":[59],"improvement":[60],"over":[61],"the":[62,71,98,123,131],"best":[64,73],"solver":[65,74,119,148],"(SBS)":[66],"closes":[68],"17-66%":[69],"of":[70,82,224],"virtual":[72],"(VBS)-SBS":[75],"gap":[76],"five":[78],"benchmarks.":[80],"Analyses":[81],"selection":[83,169,204,228],"frequencies,":[84],"margin-conditioned":[85],"reliability,":[86],"benchmark-level":[88],"oracle":[89,100,209],"structure":[90],"indicate":[91],"most":[95],"when":[97,166,225],"workflow-defined":[99,195],"landscape":[101],"has":[102],"low":[103],"winner":[104],"entropy":[105],"reasonably":[108],"separable":[109],"top-solver":[110],"region,":[111],"but":[112],"degrades":[113],"under":[114,248],"mismatch":[116],"shifts":[118],"rankings":[120],"changes":[122],"induced":[124],"labels.":[125],"These":[126],"results":[127],"suggest":[128],"that,":[129],"in":[130,147],"evaluated":[132],"regime,":[133],"robustness":[134],"limited":[136],"less":[137],"by":[138,142,253],"representational":[139,192],"capacity":[140],"than":[141],"workflow-":[143],"protocol-induced":[145,216],"instability":[146],"hierarchies,":[149],"positioning":[150],"as":[152,160,262],"in-domain":[154,246],"selector":[155,179],"for":[156,164],"fixed":[157,251],"pipelines":[158],"diagnostic":[162,222],"tool":[163],"assessing":[165],"well-posed.":[171],"Scientific":[172],"Contribution:":[173],"introduces":[175],"controlled,":[177],"embedding-based":[178],"reduces":[181],"dependence":[182,257],"on":[183],"heavy":[184],"graph":[185],"encoders,":[186],"enabling":[187],"cleaner":[189],"separation":[190],"between":[191],"choices":[193],"label":[196],"structure.":[197],"A":[198],"cross-benchmark":[199],"cross-protocol":[201],"analysis":[202],"links":[203],"success":[205],"failure":[207],"entropy,":[210],"near-ties":[211],"among":[212],"top":[213],"solvers,":[214],"ranking":[217],"shifts,":[218],"providing":[219],"evidence-backed":[221],"account":[223],"likely":[230],"yield":[232],"gains.":[233],"The":[234],"findings":[235],"differentiate":[236],"this":[237],"work":[238],"prior":[240],"AS":[242],"studies":[243],"report":[245],"improvements":[247],"workflow":[252],"explicitly":[254],"characterising":[255],"motivating":[259],"protocol-aware":[260],"modelling":[261],"route":[264],"stronger":[266],"generalisation.":[267]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-12-04T00:00:00"}
