{"id":"https://openalex.org/W4412876964","doi":"https://doi.org/10.1145/3711896.3737139","title":"Surface-based Molecular Design with Multi-modal Flow Matching","display_name":"Surface-based Molecular Design with Multi-modal Flow Matching","publication_year":2025,"publication_date":"2025-08-03","ids":{"openalex":"https://openalex.org/W4412876964","doi":"https://doi.org/10.1145/3711896.3737139"},"language":"en","primary_location":{"id":"doi:10.1145/3711896.3737139","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737139","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737139","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737139","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040225125","display_name":"Fang Wu","orcid":"https://orcid.org/0000-0001-7240-3915"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fang Wu","raw_affiliation_strings":["Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085103630","display_name":"Zhengyuan Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhengyuan Zhou","raw_affiliation_strings":["University of California, San Diego, La Jolla, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015486123","display_name":"Shuting Jin","orcid":"https://orcid.org/0000-0002-8113-9367"},"institutions":[{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuting Jin","raw_affiliation_strings":["Wuhan University of Science and Technology, Wuhan, Hubei, China"],"affiliations":[{"raw_affiliation_string":"Wuhan University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I43922553"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009424541","display_name":"Xianfa Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["Hunan University, changsha, China"],"affiliations":[{"raw_affiliation_string":"Hunan University, changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091272738","display_name":"Jure Leskovec","orcid":"https://orcid.org/0000-0002-5411-923X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jure Leskovec","raw_affiliation_strings":["Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["MoleculeMind, Beijing, Beijing, China"],"affiliations":[{"raw_affiliation_string":"MoleculeMind, Beijing, Beijing, China","institution_ids":["https://openalex.org/I78988378"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5040225125"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17931087,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3192","last_page":"3203"},"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":0.9998999834060669,"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":0.9998999834060669,"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/T10412","display_name":"Microfluidic and Capillary Electrophoresis Applications","score":0.9987999796867371,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9817000031471252,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.7092946767807007},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5867629051208496},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.5587904453277588},{"id":"https://openalex.org/keywords/flow","display_name":"Flow (mathematics)","score":0.5133683085441589},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.4308207333087921},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.1815042495727539},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1637938916683197},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.09233012795448303},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08038613200187683}],"concepts":[{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.7092946767807007},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5867629051208496},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.5587904453277588},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.5133683085441589},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.4308207333087921},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1815042495727539},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1637938916683197},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.09233012795448303},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08038613200187683},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3711896.3737139","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737139","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737139","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3711896.3737139","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3711896.3737139","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3711896.3737139","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 31st ACM SIGKDD Conference on Knowledge Discovery and Data Mining V.2","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412876964.pdf","grobid_xml":"https://content.openalex.org/works/W4412876964.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W590861535","https://openalex.org/W1991663452","https://openalex.org/W2031772330","https://openalex.org/W2073588997","https://openalex.org/W2099861795","https://openalex.org/W2101750553","https://openalex.org/W2106648157","https://openalex.org/W2161151688","https://openalex.org/W2606439133","https://openalex.org/W2874062053","https://openalex.org/W2896405912","https://openalex.org/W2990138404","https://openalex.org/W2992752586","https://openalex.org/W3082499071","https://openalex.org/W3185671814","https://openalex.org/W3213430222","https://openalex.org/W4212959738","https://openalex.org/W4220933043","https://openalex.org/W4225726305","https://openalex.org/W4236965008","https://openalex.org/W4281632800","https://openalex.org/W4376108605","https://openalex.org/W4378782828","https://openalex.org/W4390578919","https://openalex.org/W4390873054","https://openalex.org/W4391530977","https://openalex.org/W4404010963","https://openalex.org/W4404674202","https://openalex.org/W6601365666","https://openalex.org/W6609612681"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Therapeutic":[0],"peptides":[1,45],"show":[2],"promise":[3],"in":[4,13,31,108],"targeting":[5],"previously":[6],"undruggable":[7],"binding":[8,85],"sites,":[9],"with":[10],"recent":[11],"advancements":[12],"deep":[14],"generative":[15,53],"models":[16],"enabling":[17],"full-atom":[18,95],"peptide":[19,84,111,126],"co-design":[20,58],"for":[21,64,122],"specific":[22],"protein":[23,120],"receptors.However,":[24],"the":[25,88,102,115],"critical":[26],"role":[27],"of":[28,59,77,104,117],"molecular":[29,106],"surfaces":[30,107],"proteinprotein":[32],"interactions":[33],"(PPIs)":[34],"has":[35],"been":[36],"underexplored.To":[37],"bridge":[38],"this":[39],"gap,":[40],"we":[41],"propose":[42],"an":[43],"omni-design":[44],"generation":[46],"paradigm,":[47],"called":[48],"SurfFlow,":[49],"a":[50,67],"novel":[51],"surface-based":[52],"algorithm":[54],"that":[55],"enables":[56],"comprehensive":[57,89],"sequence,":[60],"structure,":[61],"and":[62,80,113],"surface":[63,78],"peptides.SurfFlow":[65],"employs":[66],"multi-modality":[68],"conditional":[69],"flow":[70],"matching":[71],"(CFM)":[72],"architecture":[73],"to":[74],"learn":[75],"distributions":[76],"geometries":[79],"biochemical":[81],"properties,":[82],"enhancing":[83],"accuracy.Evaluated":[86],"on":[87],"PepMerge":[90],"benchmark,":[91],"SurfFlow":[92],"consistently":[93],"outperforms":[94],"baselines":[96],"across":[97],"all":[98],"metrics.These":[99],"results":[100],"highlight":[101],"advantages":[103],"considering":[105],"de":[109],"novo":[110],"discovery":[112],"demonstrate":[114],"potential":[116],"integrating":[118],"multiple":[119],"modalities":[121],"more":[123],"effective":[124],"therapeutic":[125],"discovery.":[127]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}