{"id":"https://openalex.org/W4394741301","doi":"https://doi.org/10.1093/bib/bbae146","title":"SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition","display_name":"SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition","publication_year":2024,"publication_date":"2024-03-20","ids":{"openalex":"https://openalex.org/W4394741301","doi":"https://doi.org/10.1093/bib/bbae146","pmid":"https://pubmed.ncbi.nlm.nih.gov/38600663"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae146","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae146/57188966/bbae146.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae146/57188966/bbae146.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100732071","display_name":"Hui Wang","orcid":"https://orcid.org/0000-0002-4085-9050"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hui Wang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091972161","display_name":"Dong Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dong Liu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072066185","display_name":"Kailong Zhao","orcid":"https://orcid.org/0000-0003-0593-4809"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kailong Zhao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115694716","display_name":"Yajun Wang","orcid":"https://orcid.org/0000-0003-3875-6236"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yajun Wang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5049735973","display_name":"Guijun Zhang","orcid":"https://orcid.org/0000-0002-7815-5884"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guijun Zhang","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-7815-5884","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100732071"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.0551,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.75070713,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"25","issue":"3","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":0.9998000264167786,"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":0.9998000264167786,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980999827384949,"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/sequence","display_name":"Sequence (biology)","score":0.6798133850097656},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6480849385261536},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.5585082769393921},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.552688479423523},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5052266716957092},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4952634871006012},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46334108710289},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.44329798221588135},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.42970794439315796},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4240926206111908},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4173818826675415},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4133871793746948},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3920883536338806},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36620032787323},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2997809946537018},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17968079447746277},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1033293604850769},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06738761067390442}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6798133850097656},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6480849385261536},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.5585082769393921},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.552688479423523},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5052266716957092},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4952634871006012},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46334108710289},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.44329798221588135},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.42970794439315796},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4240926206111908},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4173818826675415},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4133871793746948},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3920883536338806},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36620032787323},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2997809946537018},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17968079447746277},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1033293604850769},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06738761067390442},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae146","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae146/57188966/bbae146.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38600663","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38600663","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11006797","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11006797","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11006797/pdf/bbae146.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae146","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae146/57188966/bbae146.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G320835743","display_name":null,"funder_award_id":"LZ20F030002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3775454306","display_name":null,"funder_award_id":"62173304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4569877226","display_name":null,"funder_award_id":"2022ZD0115103","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"},{"id":"https://openalex.org/G460379816","display_name":null,"funder_award_id":"LZ20F030002","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4394741301.pdf"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W146900863","https://openalex.org/W1869363046","https://openalex.org/W1954297438","https://openalex.org/W1988165326","https://openalex.org/W1997990960","https://openalex.org/W2102245393","https://openalex.org/W2620998958","https://openalex.org/W2785273668","https://openalex.org/W2790952361","https://openalex.org/W2972313406","https://openalex.org/W2991877021","https://openalex.org/W2996986155","https://openalex.org/W3010339412","https://openalex.org/W3081836708","https://openalex.org/W3087655841","https://openalex.org/W3105389349","https://openalex.org/W3106745904","https://openalex.org/W3132448805","https://openalex.org/W3175798418","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3199169486","https://openalex.org/W3200827547","https://openalex.org/W3201100749","https://openalex.org/W3211024740","https://openalex.org/W3211795435","https://openalex.org/W4205773061","https://openalex.org/W4205953903","https://openalex.org/W4210598838","https://openalex.org/W4214937996","https://openalex.org/W4223581484","https://openalex.org/W4224861788","https://openalex.org/W4283735158","https://openalex.org/W4296032638","https://openalex.org/W4297433310","https://openalex.org/W4300861364","https://openalex.org/W4319071809","https://openalex.org/W4319452608","https://openalex.org/W4323075934","https://openalex.org/W4324129409","https://openalex.org/W4389076414","https://openalex.org/W4389225229","https://openalex.org/W4389429454","https://openalex.org/W6782527804","https://openalex.org/W6810048072","https://openalex.org/W6811246986","https://openalex.org/W6838696675","https://openalex.org/W6843241131","https://openalex.org/W6849351876"],"related_works":["https://openalex.org/W2411998238","https://openalex.org/W2253761889","https://openalex.org/W2462594639","https://openalex.org/W2143233657","https://openalex.org/W3149404221","https://openalex.org/W2380350064","https://openalex.org/W2136856901","https://openalex.org/W2263295597","https://openalex.org/W1741740882","https://openalex.org/W2047083294"],"abstract_inverted_index":{"Protein":[0],"sequence":[1,15,55,62,74,79,114,138,165],"design":[2,16,75],"can":[3,57,211,239],"provide":[4],"valuable":[5],"insights":[6],"into":[7,131,241],"biopharmaceuticals":[8],"and":[9,40,110,124,154,160,181],"disease":[10],"treatments.":[11],"Currently,":[12],"most":[13],"protein":[14,45,61,73,102],"methods":[17],"based":[18,76],"on":[19,23,77,168,179],"deep":[20],"learning":[21],"focus":[22],"network":[24,136],"architecture":[25],"optimization,":[26],"while":[27],"ignoring":[28],"protein-specific":[29],"physicochemical":[30],"features.":[31],"Inspired":[32],"by":[33,193,237],"the":[34,44,51,98,113,147,194,214,227,234,242],"successful":[35],"application":[36],"of":[37,53,216],"structure":[38,46,108,117],"templates":[39],"pre-trained":[41,122],"models":[42],"in":[43,104,164,202],"prediction,":[47],"we":[48,67,207],"explored":[49],"whether":[50],"representation":[52],"structural":[54,78,121,228],"profile":[56,80,115],"be":[58],"used":[59],"for":[60,72,100,137],"design.":[63],"In":[64],"this":[65],"work,":[66],"propose":[68],"SPDesign,":[69],"a":[70],"method":[71],"using":[81],"ultrafast":[82,92],"shape":[83,93],"recognition.":[84],"Given":[85],"an":[86,132],"input":[87],"backbone":[88],"structure,":[89],"SPDesign":[90,144,199,210,238],"utilizes":[91],"recognition":[94],"vectors":[95],"to":[96,157],"accelerate":[97],"search":[99],"similar":[101,221],"structures":[103,222,244],"our":[105],"in-house":[106],"PAcluster80":[107],"database":[109],"then":[111],"extracts":[112],"through":[116],"alignment.":[118],"Combined":[119],"with":[120,186],"knowledge":[123],"geometric":[125],"features,":[126],"they":[127],"are":[128],"further":[129],"fed":[130],"enhanced":[133],"graph":[134],"neural":[135],"prediction.":[139],"The":[140],"results":[141,174],"show":[142],"that":[143,198,209,219,233],"significantly":[145],"outperforms":[146],"state-of-the-art":[148],"methods,":[149],"such":[150],"as":[151],"ProteinMPNN,":[152],"Pifold":[153],"LM-Design,":[155],"leading":[156],"21.89%,":[158],"15.54%":[159],"11.4%":[161],"accuracy":[162],"gains":[163],"recovery":[166],"rate":[167],"CATH":[169],"4.2":[170],"benchmark,":[171],"respectively.":[172],"Encouraging":[173],"also":[175],"have":[176,220],"been":[177],"achieved":[178],"orphan":[180],"de":[182],"novo":[183],"(designed)":[184],"benchmarks":[185],"few":[187],"homologous":[188],"sequences.":[189,225],"Furthermore,":[190],"analysis":[191],"conducted":[192],"PDBench":[195],"tool":[196],"suggests":[197],"performs":[200],"well":[201,212],"subdivided":[203],"structures.":[204],"More":[205],"interestingly,":[206],"found":[208],"reconstruct":[213],"sequences":[215,235],"some":[217],"proteins":[218],"but":[223],"different":[224],"Finally,":[226],"modeling":[229],"verification":[230],"experiment":[231],"indicates":[232],"designed":[236],"fold":[240],"native":[243],"more":[245],"accurately.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}