{"id":"https://openalex.org/W4319452608","doi":"https://doi.org/10.48550/arxiv.2302.02277","title":"SE(3) diffusion model with application to protein backbone generation","display_name":"SE(3) diffusion model with application to protein backbone generation","publication_year":2023,"publication_date":"2023-02-05","ids":{"openalex":"https://openalex.org/W4319452608","doi":"https://doi.org/10.48550/arxiv.2302.02277"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2302.02277","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2302.02277","pdf_url":"https://arxiv.org/pdf/2302.02277","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2302.02277","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074628247","display_name":"Jason Yim","orcid":"https://orcid.org/0000-0003-0575-7400"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yim, Jason","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061922457","display_name":"Brian L. Trippe","orcid":"https://orcid.org/0000-0002-6901-4676"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Trippe, Brian L.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050614717","display_name":"Valentin De Bortoli","orcid":"https://orcid.org/0000-0002-7163-5391"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"De Bortoli, Valentin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051016788","display_name":"\u00c9mile Mathieu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mathieu, Emile","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091677854","display_name":"Randal Douc","orcid":"https://orcid.org/0000-0003-3910-9495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Doucet, Arnaud","raw_affiliation_strings":[],"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":[],"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":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5074628247"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":71,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9894000291824341,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9894000291824341,"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/T11124","display_name":"Protein purification and stability","score":0.982200026512146,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9782999753952026,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/invariant","display_name":"Invariant (physics)","score":0.5997017025947571},{"id":"https://openalex.org/keywords/monomer","display_name":"Monomer","score":0.5728681683540344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5345871448516846},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4505864977836609},{"id":"https://openalex.org/keywords/frame-work","display_name":"Frame work","score":0.4501835107803345},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43976449966430664},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4373599588871002},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4051598012447357},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3757586181163788},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32276904582977295},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2792521119117737},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2700890004634857},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.15730974078178406},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11084714531898499},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10162308812141418}],"concepts":[{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.5997017025947571},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.5728681683540344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5345871448516846},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4505864977836609},{"id":"https://openalex.org/C3018407679","wikidata":"https://www.wikidata.org/wiki/Q1289773","display_name":"Frame work","level":2,"score":0.4501835107803345},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43976449966430664},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4373599588871002},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4051598012447357},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3757586181163788},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32276904582977295},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2792521119117737},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2700890004634857},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.15730974078178406},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11084714531898499},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10162308812141418},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C109214941","wikidata":"https://www.wikidata.org/wiki/Q18334","display_name":"Particle physics","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2302.02277","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2302.02277","pdf_url":"https://arxiv.org/pdf/2302.02277","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2302.02277","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2302.02277","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2302.02277","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2302.02277","pdf_url":"https://arxiv.org/pdf/2302.02277","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1871434800","display_name":null,"funder_award_id":"EP/R034710/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3402893575","display_name":null,"funder_award_id":"EP/R018561/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319452608.pdf","grobid_xml":"https://content.openalex.org/works/W4319452608.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2357692583","https://openalex.org/W2045488530","https://openalex.org/W4387781933","https://openalex.org/W2045468340","https://openalex.org/W2374513464","https://openalex.org/W1979677112","https://openalex.org/W2912217925","https://openalex.org/W760974036","https://openalex.org/W2036222533","https://openalex.org/W2381549039"],"abstract_inverted_index":{"The":[0],"design":[1],"of":[2,21,64,88,152],"novel":[3,99],"protein":[4,10,42,135,157],"structures":[5],"remains":[6],"a":[7,23,98,133],"challenge":[8],"in":[9,29,38,49,69],"engineering":[11],"for":[12,58,102],"applications":[13],"across":[14],"biomedicine":[15],"and":[16,75,118],"chemistry.":[17],"In":[18],"this":[19],"line":[20],"work,":[22],"diffusion":[24,59,91],"model":[25],"over":[26,108],"rigid":[27,67],"bodies":[28],"3D":[30],"(referred":[31],"to":[32,126,143],"as":[33],"frames)":[34],"has":[35,140],"shown":[36],"success":[37],"generating":[39],"novel,":[40],"functional":[41],"backbones":[43],"that":[44,71,139],"have":[45],"not":[46],"been":[47,141],"observed":[48],"nature.":[50],"However,":[51],"there":[52],"exists":[53],"no":[54],"principled":[55],"methodological":[56],"framework":[57],"on":[60,73,93,114,132],"SE(3),":[61],"the":[62,77,104],"space":[63],"orientation":[65],"preserving":[66],"motions":[68],"R3,":[70],"operates":[72],"frames":[74,95],"confers":[76],"group":[78],"invariance.":[79],"We":[80,111,146],"address":[81],"these":[82],"shortcomings":[83],"by":[84,97],"developing":[85],"theoretical":[86],"foundations":[87],"SE(3)":[89,105],"invariant":[90],"models":[92],"multiple":[94,109],"followed":[96],"framework,":[100],"FrameDiff,":[101],"learning":[103],"equivariant":[106],"score":[107],"frames.":[110],"apply":[112],"FrameDiff":[113],"monomer":[115],"backbone":[116],"generation":[117],"find":[119,147],"it":[120],"can":[121],"generate":[122],"designable":[123],"monomers":[124],"up":[125],"500":[127],"amino":[128],"acids":[129],"without":[130],"relying":[131],"pretrained":[134],"structure":[136],"prediction":[137],"network":[138],"integral":[142],"previous":[144],"methods.":[145],"our":[148],"samples":[149],"are":[150],"capable":[151],"generalizing":[153],"beyond":[154],"any":[155],"known":[156],"structure.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":23},{"year":2024,"cited_by_count":36},{"year":2023,"cited_by_count":10}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
