{"id":"https://openalex.org/W7154038434","doi":"https://doi.org/10.48550/arxiv.2604.09540","title":"A Physically-Informed Subgraph Isomorphism Approach to Molecular Docking Using Quantum Annealers","display_name":"A Physically-Informed Subgraph Isomorphism Approach to Molecular Docking Using Quantum Annealers","publication_year":2026,"publication_date":"2026-04-10","ids":{"openalex":"https://openalex.org/W7154038434","doi":"https://doi.org/10.48550/arxiv.2604.09540"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.09540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.09540","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.09540","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119668914","display_name":"Francesco Micucci","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Micucci, Francesco","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133476168","display_name":"Matteo Barbieri","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Barbieri, Matteo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065426830","display_name":"Gabriella Bettonte","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bettonte, Gabriella","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074637397","display_name":"Domenico Bonanni","orcid":"https://orcid.org/0000-0001-9160-0914"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bonanni, Domenico","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058639297","display_name":"Anita Camillini","orcid":"https://orcid.org/0000-0002-9966-4426"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Camillini, Anita","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133504728","display_name":"Anna Fava","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fava, Anna","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101821783","display_name":"Daniele Gregori","orcid":"https://orcid.org/0000-0002-6137-6453"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gregori, Daniele","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133522197","display_name":"Andrea R. Beccari","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Beccari, Andrea R.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5107950551","display_name":"Gianluca Palermo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Palermo, Gianluca","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5119668914"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.20399999618530273,"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"}},"topics":[{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.20399999618530273,"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/T10682","display_name":"Quantum Computing Algorithms and Architecture","score":0.15719999372959137,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.1395999938249588,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/graph-isomorphism","display_name":"Graph isomorphism","score":0.5350000262260437},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4991999864578247},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.48420000076293945},{"id":"https://openalex.org/keywords/quantum-annealing","display_name":"Quantum annealing","score":0.47609999775886536},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4284999966621399},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.4124999940395355},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.3919999897480011},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.37630000710487366}],"concepts":[{"id":"https://openalex.org/C61665672","wikidata":"https://www.wikidata.org/wiki/Q303100","display_name":"Graph isomorphism","level":4,"score":0.5350000262260437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.501800000667572},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4991999864578247},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.48420000076293945},{"id":"https://openalex.org/C90408235","wikidata":"https://www.wikidata.org/wiki/Q938141","display_name":"Quantum annealing","level":4,"score":0.47609999775886536},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4284999966621399},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.4124999940395355},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.3919999897480011},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.37630000710487366},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.37540000677108765},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.33980000019073486},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3257000148296356},{"id":"https://openalex.org/C203436722","wikidata":"https://www.wikidata.org/wiki/Q902950","display_name":"Isomorphism (crystallography)","level":3,"score":0.30809998512268066},{"id":"https://openalex.org/C133956753","wikidata":"https://www.wikidata.org/wiki/Q583864","display_name":"FKBP","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.298799991607666},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.28439998626708984},{"id":"https://openalex.org/C73000952","wikidata":"https://www.wikidata.org/wiki/Q17007827","display_name":"Discretization","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.27079999446868896},{"id":"https://openalex.org/C2991951333","wikidata":"https://www.wikidata.org/wiki/Q188403","display_name":"Quantum chemical","level":3,"score":0.26269999146461487},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.25850000977516174},{"id":"https://openalex.org/C58053490","wikidata":"https://www.wikidata.org/wiki/Q176555","display_name":"Quantum computer","level":3,"score":0.2563999891281128}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.09540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.09540","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.09540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.09540","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Molecular":[0],"docking":[1,139,197],"is":[2],"a":[3,18,26,32,80,144],"crucial":[4],"step":[5],"in":[6],"the":[7,15,23,30,36,51,54,66,84,88,94,98,104,107,111,118,126,130,135,138,173,184,193,196],"development":[8],"of":[9,17,25,38,87,93,137,195],"new":[10],"drugs":[11],"as":[12,70,169],"it":[13],"guides":[14],"positioning":[16],"small":[19],"molecule":[20],"(ligand)":[21],"within":[22],"pocket":[24,100],"target":[27],"protein.":[28],"In":[29],"literature,":[31],"feasibility":[33],"study":[34,120],"explored":[35],"potential":[37],"D-Wave":[39,185],"quantum":[40,186],"annealers":[41,187],"for":[42],"purely":[43,175],"geometric":[44,74,176],"molecular":[45],"docking,":[46],"neglecting":[47],"physicochemical":[48,123],"interactions":[49,124,168],"between":[50,106,125],"protein":[52,89,99],"and":[53,56,76,110,151,161,179],"ligand":[55,95,108],"focusing":[57],"solely":[58],"on":[59,97,117,192],"their":[60,73,190],"simplified":[61],"geometries.":[62],"To":[63],"achieve":[64],"this,":[65],"ligands":[67],"were":[68],"represented":[69],"graphs":[71],"incorporating":[72],"properties":[75],"then":[77],"mapped":[78],"onto":[79],"grid":[81],"that":[82,148],"discretized":[83],"three-dimensional":[85],"space":[86],"pocket.":[90],"The":[91],"quality":[92],"pose":[96],"was":[101],"evaluated":[102],"through":[103],"isomorphism":[105],"graph":[109],"spatial":[112],"grid.":[113],"This":[114,141],"paper":[115,142],"builds":[116],"previous":[119,174],"by":[121],"introducing":[122],"protein-ligand":[127],"pair":[128],"into":[129],"QUBO":[131,146,177],"problem":[132],"to":[133,172,188],"improve":[134],"accuracy":[136,194],"results.":[140,198],"presents":[143],"novel":[145],"formulation":[147],"includes":[149],"Coulomb":[150],"van":[152],"der":[153],"Waals":[154],"forces,":[155],"together":[156],"with":[157],"components":[158],"representing":[159],"H-bond":[160],"hydrophobic":[162],"interactions.":[163],"We":[164],"integrate":[165],"these":[166],"physical":[167],"corrective":[170],"terms":[171],"formulation,":[178],"provide":[180],"experimental":[181],"results":[182],"using":[183],"demonstrate":[189],"impact":[191]},"counts_by_year":[],"updated_date":"2026-05-04T08:30:34.212998","created_date":"2026-04-14T00:00:00"}