{"id":"https://openalex.org/W7208760369","doi":"https://doi.org/10.26434/chemrxiv.15008308/v1","title":"Learning Multiscale Computational Strategies for Supramolecular Recognition","display_name":"Learning Multiscale Computational Strategies for Supramolecular Recognition","publication_year":2026,"publication_date":"2026-09-04","ids":{"openalex":"https://openalex.org/W7208760369","doi":"https://doi.org/10.26434/chemrxiv.15008308/v1"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv.15008308/v1","doi":"https://doi.org/10.26434/chemrxiv.15008308/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15008308/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008308/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008308/v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102986502","display_name":"Wenting Tang","orcid":"https://orcid.org/0009-0009-5801-6586","observed_orcids":["https://orcid.org/0009-0009-5801-6586"]},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenting Tang","raw_affiliation_strings":["Beihang University","School of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beihang University","institution_ids":["https://openalex.org/I82880672"]},{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143420306","display_name":"Zhenhua Lu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]},{"id":"https://openalex.org/I4405255904","display_name":"Shenzhen University of Advanced Technology","ror":"https://ror.org/03hz5th67","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405255904"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenhua Lu","raw_affiliation_strings":["College of Life Sciences","Faculty of Synthetic Biology","Nankai University","Shenzhen University of Advanced Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences","institution_ids":[]},{"raw_affiliation_string":"Faculty of Synthetic Biology","institution_ids":[]},{"raw_affiliation_string":"Nankai University","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"Shenzhen University of Advanced Technology","institution_ids":["https://openalex.org/I4405255904"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055111785","display_name":"Lizhen Huo","orcid":"https://orcid.org/0009-0002-1739-9858","observed_orcids":["https://orcid.org/0009-0002-1739-9858","https://orcid.org/0009-0001-5089-5493"]},"institutions":[{"id":"https://openalex.org/I3045169105","display_name":"Southern University of Science and Technology","ror":"https://ror.org/049tv2d57","country_code":"CN","type":"education","lineage":["https://openalex.org/I3045169105"]},{"id":"https://openalex.org/I4405255904","display_name":"Shenzhen University of Advanced Technology","ror":"https://ror.org/03hz5th67","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405255904"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lizhen Huo","raw_affiliation_strings":["Department of Biomedical Engineering","Faculty of Synthetic Biology","Shenzhen University of Advanced Technology","Southern University of Science and Technology"],"raw_orcid":"https://orcid.org/0009-0002-1739-9858","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering","institution_ids":[]},{"raw_affiliation_string":"Faculty of Synthetic Biology","institution_ids":[]},{"raw_affiliation_string":"Shenzhen University of Advanced Technology","institution_ids":["https://openalex.org/I4405255904"]},{"raw_affiliation_string":"Southern University of Science and Technology","institution_ids":["https://openalex.org/I3045169105"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124998508","display_name":"Zhixuan Huang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I3045169105","display_name":"Southern University of Science and Technology","ror":"https://ror.org/049tv2d57","country_code":"CN","type":"education","lineage":["https://openalex.org/I3045169105"]},{"id":"https://openalex.org/I4405255904","display_name":"Shenzhen University of Advanced Technology","ror":"https://ror.org/03hz5th67","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405255904"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixuan Huang","raw_affiliation_strings":["Department of Biomedical Engineering","Faculty of Synthetic Biology","Shenzhen University of Advanced Technology","Southern University of Science and Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering","institution_ids":[]},{"raw_affiliation_string":"Faculty of Synthetic Biology","institution_ids":[]},{"raw_affiliation_string":"Shenzhen University of Advanced Technology","institution_ids":["https://openalex.org/I4405255904"]},{"raw_affiliation_string":"Southern University of Science and Technology","institution_ids":["https://openalex.org/I3045169105"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5150023479","display_name":"Yang Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I34949971","display_name":"University of Jinan","ror":"https://ror.org/02mjz6f26","country_code":"CN","type":"education","lineage":["https://openalex.org/I34949971"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["School of Physics and Technology","University of Jinan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physics and Technology","institution_ids":[]},{"raw_affiliation_string":"University of Jinan","institution_ids":["https://openalex.org/I34949971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000677558","display_name":"Zuo-Yuan Zhang","orcid":"https://orcid.org/0009-0009-3686-6870","observed_orcids":["https://orcid.org/0009-0009-3686-6870"]},"institutions":[{"id":"https://openalex.org/I78978612","display_name":"Yangzhou University","ror":"https://ror.org/03tqb8s11","country_code":"CN","type":"education","lineage":["https://openalex.org/I78978612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zuo-yuan Zhang","raw_affiliation_strings":["School of Physical Science and Technology","Yangzhou University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physical Science and Technology","institution_ids":[]},{"raw_affiliation_string":"Yangzhou University","institution_ids":["https://openalex.org/I78978612"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070063506","display_name":"Zhaoxi Sun","orcid":"https://orcid.org/0000-0001-8311-7797","observed_orcids":["https://orcid.org/0000-0001-8311-7797"]},"institutions":[{"id":"https://openalex.org/I4405255904","display_name":"Shenzhen University of Advanced Technology","ror":"https://ror.org/03hz5th67","country_code":"CN","type":"education","lineage":["https://openalex.org/I4405255904"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoxi Sun","raw_affiliation_strings":["Faculty of Synthetic Biology","Shenzhen University of Advanced Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Synthetic Biology","institution_ids":[]},{"raw_affiliation_string":"Shenzhen University of Advanced Technology","institution_ids":["https://openalex.org/I4405255904"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10578","display_name":"Supramolecular Chemistry and Complexes","score":0.8935999870300293,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10578","display_name":"Supramolecular Chemistry and Complexes","score":0.8935999870300293,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.08470000326633453,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/host-guest-binding-affinity","display_name":"host-guest binding affinity","score":0.8690000176429749},{"id":"https://openalex.org/keywords/supramolecular-recognition","display_name":"supramolecular recognition","score":0.9290000200271606},{"id":"https://openalex.org/keywords/mm-gbsa","display_name":"MM-GBSA","score":0.7609999775886536},{"id":"https://openalex.org/keywords/implicit-solvent-models","display_name":"implicit solvent","score":0.7760000228881836},{"id":"https://openalex.org/keywords/pillararenes","display_name":"pillararenes","score":0.7630000114440918},{"id":"https://openalex.org/keywords/cucurbituril","display_name":"cucurbituril","score":0.9990000128746033},{"id":"https://openalex.org/keywords/cyclodextrins","display_name":"cyclodextrins","score":0.996999979019165},{"id":"https://openalex.org/keywords/accuracy-cost-trade-off","display_name":"accuracy-cost trade-off","score":0.9100000262260437},{"id":"https://openalex.org/keywords/pareto-analysis","display_name":"Pareto analysis","score":0.7860000133514404},{"id":"https://openalex.org/keywords/decision-tree-modeling","display_name":"decision tree modeling","score":0.7009999752044678}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.64410001039505},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5587999820709229},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4855000078678131},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.47350001335144043},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.4325000047683716},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42649999260902405},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.398499995470047},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3871000111103058},{"id":"https://openalex.org/C93275456","wikidata":"https://www.wikidata.org/wiki/Q756449","display_name":"Supramolecular chemistry","level":3,"score":0.3578000068664551},{"id":"https://openalex.org/C171752962","wikidata":"https://www.wikidata.org/wiki/Q255166","display_name":"Kullback\u2013Leibler divergence","level":2,"score":0.3562999963760376},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3296000063419342},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.3276999890804291},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3149999976158142},{"id":"https://openalex.org/C52622258","wikidata":"https://www.wikidata.org/wiki/Q131222","display_name":"Information theory","level":2,"score":0.2892000079154968},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.28040000796318054},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.2754000127315521},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2660999894142151},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.265500009059906},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.2646999955177307},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26350000500679016},{"id":"https://openalex.org/C13460635","wikidata":"https://www.wikidata.org/wiki/Q85753676","display_name":"Classification scheme","level":2,"score":0.26100000739097595},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.25929999351501465}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv.15008308/v1","doi":"https://doi.org/10.26434/chemrxiv.15008308/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15008308/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008308/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv.15008308/v1","doi":"https://doi.org/10.26434/chemrxiv.15008308/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15008308/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15008308/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1343958019","display_name":null,"funder_award_id":"25DX2800500","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G5290221938","display_name":null,"funder_award_id":"62305285","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7208760369.pdf","grobid_xml":"https://content.openalex.org/works/W7208760369.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2087271871","https://openalex.org/W2951039542","https://openalex.org/W2923271510","https://openalex.org/W2021827099","https://openalex.org/W4309244869","https://openalex.org/W4387909007","https://openalex.org/W3092613274","https://openalex.org/W4327983909","https://openalex.org/W4296982331","https://openalex.org/W4412647737"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,228],"of":[2,28,45,108,125,187,215],"host-guest":[3,53],"binding":[4],"affinities":[5],"with":[6,86,122],"end-point":[7,46,216],"free":[8],"energy":[9],"approaches":[10],"requires":[11],"a":[12,42,148,165,203,220],"balance":[13,171],"between":[14,172],"molecular":[15],"sampling,":[16,69],"energetic":[17],"description,":[18],"and":[19,26,60,66,76,79,82,127,168,174,180,198,225],"computational":[20,175,217],"cost,":[21],"yet":[22],"the":[23,105,119],"relative":[24],"importance":[25],"interplay":[27],"these":[29],"factors":[30],"remain":[31],"poorly":[32],"understood":[33],"for":[34,206,222],"chemically":[35],"diverse":[36],"supramolecular":[37,230],"systems.":[38],"Here,":[39],"we":[40],"establish":[41,202],"systematic":[43,140,185],"benchmark":[44],"affinity":[47,101,132,227],"calculations":[48],"across":[49],"more":[50,223],"than":[51],"300":[52],"pairs":[54],"involving":[55],"pillararenes,":[56],"cucurbiturils,":[57],"octa":[58],"acid,":[59],"cyclodextrins.":[61],"We":[62,90],"systematically":[63],"evaluate":[64],"single-(1T)":[65],"three-trajectory":[67],"(3T)":[68],"harmonic":[70],"entropy":[71,137],"corrections,":[72],"multiple":[73],"extended":[74],"tight-binding":[75],"DFT":[77,154],"levels,":[78],"implicit-solvent":[80],"treatments,":[81],"then":[83],"compare":[84],"them":[85],"established":[87],"MM/GBSA":[88,160],"protocols.":[89],"find":[91],"that":[92,104],"different":[93],"electronic-structure":[94],"treatments":[95],"can":[96],"produce":[97],"substantially":[98],"different,":[99],"host-dependent":[100],"landscapes,":[102],"underscoring":[103],"nominal":[106],"level":[107],"theory":[109],"alone":[110],"is":[111],"insufficient":[112],"to":[113],"determine":[114],"predictive":[115,158],"reliability.":[116],"In":[117],"contrast,":[118],"3T":[120],"scheme":[121],"independent":[123],"sampling":[124],"bound":[126],"unbound":[128],"states":[129],"consistently":[130],"improves":[131],"prediction,":[133],"whereas":[134],"MM-based":[135],"normal-mode":[136],"provides":[138,164],"little":[139],"benefit.":[141],"A":[142],"multi-objective":[143],"Pareto":[144],"analysis":[145,179],"further":[146],"reveals":[147],"pronounced":[149],"accuracy-cost":[150],"trade-off:":[151],"although":[152],"selected":[153],"protocols":[155],"achieve":[156],"high":[157],"accuracy,":[159],"2":[161],"/":[162],"26":[163],"remarkably":[166],"favorable":[167],"broadly":[169],"transferable":[170],"accuracy":[173],"expense.":[176],"Finally,":[177],"host-wise":[178],"interpretable":[181],"decision-tree":[182],"modeling":[183],"reveal":[184],"dependence":[186],"protocol":[188],"preference":[189],"on":[190],"readily":[191],"accessible":[192],"host":[193,196],"descriptors,":[194],"particularly":[195],"charge":[197],"size.":[199],"These":[200],"results":[201],"practical":[204],"framework":[205],"moving":[207],"from":[208],"universal":[209],"method":[210],"benchmarking":[211],"toward":[212],"host-aware":[213],"selection":[214],"protocols,":[218],"providing":[219],"basis":[221],"efficient":[224],"adaptive":[226],"in":[229],"chemistry.":[231]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-05T00:00:00"}