{"id":"https://openalex.org/W4382765830","doi":"https://doi.org/10.48550/arxiv.2306.16819","title":"Graph Denoising Diffusion for Inverse Protein Folding","display_name":"Graph Denoising Diffusion for Inverse Protein Folding","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4382765830","doi":"https://doi.org/10.48550/arxiv.2306.16819"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2306.16819","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},"type":"preprint","type_crossref":"posted-content","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/abs/2306.16819","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100765686","display_name":"Kai Yi","orcid":"https://orcid.org/0000-0003-0415-3584"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yi, Kai","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027695625","display_name":"Bingxin Zhou","orcid":"https://orcid.org/0000-0002-3897-9766"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhou, Bingxin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072622467","display_name":"Yiqing Shen","orcid":"https://orcid.org/0000-0001-7866-3339"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shen, Yiqing","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li\u00f2, Pietro","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5070236689","display_name":"Yu Guang Wang","orcid":"https://orcid.org/0000-0002-7450-0273"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Yu Guang","raw_affiliation_strings":[],"affiliations":[]}],"institution_assertions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.999974,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995,"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":0.9995,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9908,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.51618534},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.44879594},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein Engineering","score":0.4110723}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.58971196},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.52415466},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.51618534},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.510226},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.44879594},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.42979604},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.41507018},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.41168013},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.4110723},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39652017},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.38488552},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36449057},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.35730076},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32993376},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3224014},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24067858},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14993885},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2306.16819","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://api.datacite.org/dois/10.48550/arxiv.2306.16819","pdf_url":null,"source":{"id":"https://openalex.org/S4393179698","display_name":"DataCite API","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210145204","host_organization_name":"DataCite","host_organization_lineage":["https://openalex.org/I4210145204"],"host_organization_lineage_names":["DataCite"],"type":"metadata"},"license":null,"license_id":null,"version":null}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2306.16819","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},"sustainable_development_goals":[{"score":0.74,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4394728283","https://openalex.org/W4390874210","https://openalex.org/W4388844349","https://openalex.org/W4386184937","https://openalex.org/W4384918963","https://openalex.org/W2153939756","https://openalex.org/W2128027845","https://openalex.org/W2105231718","https://openalex.org/W2093104230","https://openalex.org/W1493875009"],"abstract_inverted_index":{"Inverse":[0],"protein":[1,24,86,98,103,195,200],"folding":[2],"is":[3],"challenging":[4],"due":[5],"to":[6,53,76],"its":[7],"inherent":[8],"one-to-many":[9],"mapping":[10],"characteristic,":[11],"where":[12,100],"numerous":[13],"possible":[14],"amino":[15,112,123,137,152],"acid":[16,113,138],"sequences":[17,33,196],"can":[18],"fold":[19],"into":[20],"a":[21,78,90,101,179,198],"single,":[22],"identical":[23],"backbone.":[25],"This":[26],"task":[27],"involves":[28],"not":[29],"only":[30],"identifying":[31],"viable":[32],"but":[34],"also":[35],"representing":[36],"the":[37,55,74,106,110,119,127,142,147,166,170],"sheer":[38],"diversity":[39],"of":[40,58,70,81,122,151,169,181],"potential":[41,75,191],"solutions.":[42,60],"However,":[43],"existing":[44],"discriminative":[45],"models,":[46,51,65],"such":[47],"as":[48,66,160,162],"transformer-based":[49],"auto-regressive":[50],"struggle":[52],"encapsulate":[54],"diverse":[56,79,194],"range":[57],"plausible":[59],"In":[61],"contrast,":[62],"diffusion":[63,94,107,143],"probabilistic":[64],"an":[67],"emerging":[68],"genre":[69],"generative":[71,171],"approaches,":[72],"offer":[73],"generate":[77],"set":[80,180],"sequence":[82,186],"candidates":[83],"for":[84,96,141,197],"determined":[85,199],"backbones.":[87],"We":[88],"propose":[89],"novel":[91],"graph":[92],"denoising":[93],"model":[95,117,174],"inverse":[97],"folding,":[99],"given":[102],"backbone":[104,201],"guides":[105],"process":[108],"on":[109,126],"corresponding":[111],"residue":[114],"types.":[115],"The":[116],"infers":[118],"joint":[120],"distribution":[121],"acids":[124,153],"conditioned":[125],"nodes'":[128],"physiochemical":[129],"properties":[130],"and":[131,157,188],"local":[132],"environment.":[133],"Moreover,":[134],"we":[135],"utilize":[136],"replacement":[139],"matrices":[140],"forward":[144],"process,":[145],"encoding":[146],"biologically-meaningful":[148],"prior":[149],"knowledge":[150],"from":[154],"their":[155],"spatial":[156],"sequential":[158],"neighbors":[159],"well":[161],"themselves,":[163],"which":[164],"reduces":[165],"sampling":[167],"space":[168],"process.":[172],"Our":[173],"achieves":[175],"state-of-the-art":[176],"performance":[177],"over":[178],"popular":[182],"baseline":[183],"methods":[184],"in":[185,192],"recovery":[187],"exhibits":[189],"great":[190],"generating":[193],"structure.":[202]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4382765830","counts_by_year":[{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3}],"updated_date":"2025-01-04T17:38:35.268869","created_date":"2023-07-01"}