{"id":"https://openalex.org/W4387560352","doi":"https://doi.org/10.48550/arxiv.2310.05764","title":"Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design","display_name":"Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design","publication_year":2023,"publication_date":"2023-10-09","ids":{"openalex":"https://openalex.org/W4387560352","doi":"https://doi.org/10.48550/arxiv.2310.05764"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2310.05764","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2310.05764","pdf_url":"https://arxiv.org/pdf/2310.05764","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2310.05764","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088533003","display_name":"H. St\u00e4rk","orcid":"https://orcid.org/0000-0002-4463-326X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"St\u00e4rk, Hannes","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074077264","display_name":"Bowen Jing","orcid":"https://orcid.org/0000-0003-0843-6979"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jing, Bowen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010124873","display_name":"Regina Barzilay","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Barzilay, Regina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5048915657","display_name":"Tommi Jaakkola","orcid":"https://orcid.org/0000-0002-2199-0379"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jaakkola, Tommi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":7,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9905999898910522,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9905999898910522,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.9143999814987183,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T10839","display_name":"Pancreatic function and diabetes","score":0.9132000207901001,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6324858665466309},{"id":"https://openalex.org/keywords/generality","display_name":"Generality","score":0.5370418429374695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46148744225502014},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.44452333450317383},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.41294509172439575},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4018544554710388},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.38683900237083435},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11669892072677612},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08445814251899719}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6324858665466309},{"id":"https://openalex.org/C2780767217","wikidata":"https://www.wikidata.org/wiki/Q5532421","display_name":"Generality","level":2,"score":0.5370418429374695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46148744225502014},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.44452333450317383},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.41294509172439575},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4018544554710388},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38683900237083435},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11669892072677612},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08445814251899719},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","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/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2310.05764","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2310.05764","pdf_url":"https://arxiv.org/pdf/2310.05764","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2310.05764","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2310.05764","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"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2310.05764","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2310.05764","pdf_url":"https://arxiv.org/pdf/2310.05764","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"score":0.8700000047683716,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387560352.pdf","grobid_xml":"https://content.openalex.org/works/W4387560352.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2045049461","https://openalex.org/W1978893398","https://openalex.org/W2201908702","https://openalex.org/W4381094582","https://openalex.org/W2369625323","https://openalex.org/W2364579609","https://openalex.org/W3143642740","https://openalex.org/W4214840794","https://openalex.org/W4285478100","https://openalex.org/W2167226024"],"abstract_inverted_index":{"A":[0],"significant":[1],"amount":[2],"of":[3],"protein":[4,64],"function":[5],"requires":[6],"binding":[7,16,46,72,103],"small":[8,19],"molecules,":[9],"including":[10],"enzymatic":[11],"catalysis.":[12],"As":[13],"such,":[14],"designing":[15],"pockets":[17],"for":[18,84],"molecules":[20],"has":[21],"several":[22],"impactful":[23],"applications":[24],"ranging":[25],"from":[26],"drug":[27],"synthesis":[28],"to":[29,60],"energy":[30],"storage.":[31],"Towards":[32],"this":[33,57,98],"goal,":[34],"we":[35],"first":[36],"develop":[37],"HarmonicFlow,":[38],"an":[39],"improved":[40],"generative":[41,82],"process":[42],"over":[43],"3D":[44,73],"protein-ligand":[45],"structures":[47],"based":[48],"on":[49],"our":[50],"self-conditioned":[51],"flow":[52,58],"matching":[53],"objective.":[54],"FlowSite":[55,101],"extends":[56],"model":[59],"jointly":[61],"generate":[62],"a":[63],"pocket's":[65],"discrete":[66],"residue":[67],"types":[68],"and":[69,89],"the":[70],"molecule's":[71],"structure.":[74],"We":[75],"show":[76],"that":[77],"HarmonicFlow":[78],"improves":[79],"upon":[80],"state-of-the-art":[81],"processes":[83],"docking":[85],"in":[86,93],"simplicity,":[87],"generality,":[88],"average":[90],"sample":[91],"quality":[92],"pocket-level":[94],"docking.":[95],"Enabled":[96],"by":[97],"structure":[99],"modeling,":[100],"designs":[102],"sites":[104],"substantially":[105],"better":[106],"than":[107],"baseline":[108],"approaches.":[109]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2023-10-12T00:00:00"}