{"id":"https://openalex.org/W4389429454","doi":"https://doi.org/10.1371/journal.pcbi.1011330","title":"SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network","display_name":"SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network","publication_year":2023,"publication_date":"2023-12-07","ids":{"openalex":"https://openalex.org/W4389429454","doi":"https://doi.org/10.1371/journal.pcbi.1011330","pmid":"https://pubmed.ncbi.nlm.nih.gov/38060617"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011330","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011330","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011330","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067129527","display_name":"Xing Zhang","orcid":"https://orcid.org/0000-0001-8902-0355"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]},{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xing Zhang","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China","School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0001-8902-0355","affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hongmei Yin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongmei Yin","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084697054","display_name":"Fei Ling","orcid":null},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fei Ling","raw_affiliation_strings":["School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biology and Biological Engineering, South China University of Technology, Guangzhou, People's Republic of China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071120707","display_name":"Jian Zhan","orcid":"https://orcid.org/0000-0003-0856-2385"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian Zhan","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032724151","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0002-9958-5699"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China"],"raw_orcid":"https://orcid.org/0000-0002-9958-5699","affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, People's Republic of China","institution_ids":["https://openalex.org/I4210102541"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032724151","https://openalex.org/A5067129527","https://openalex.org/A5071120707","https://openalex.org/A5084697054"],"corresponding_institution_ids":["https://openalex.org/I4210102541","https://openalex.org/I90610280"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.0203,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.87044224,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"19","issue":"12","first_page":"e1011330","last_page":"e1011330"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9958999752998352,"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":0.9958999752998352,"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/graph","display_name":"Graph","score":0.5569632649421692},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.46226465702056885},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4287794232368469},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3497771620750427},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.29437798261642456},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2772895097732544},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20588967204093933}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5569632649421692},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.46226465702056885},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4287794232368469},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3497771620750427},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.29437798261642456},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2772895097732544},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20588967204093933}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011330","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011330","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:38060617","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38060617","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10729952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10729952","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10729952/pdf/pcbi.1011330.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:035b7de7b1274050aa50d6120d75200c","is_oa":true,"landing_page_url":"https://doaj.org/article/035b7de7b1274050aa50d6120d75200c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 12, p e1011330 (2023)","raw_type":"article"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/427829","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/427829","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"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":"Journal article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011330","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011330","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1385649608","display_name":null,"funder_award_id":"2021YFF1200400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G174779700","display_name":null,"funder_award_id":"NO.2021YFF1200400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7865030205","display_name":null,"funder_award_id":". 2021YFF1200400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G962820005","display_name":null,"funder_award_id":"S201101001","funder_id":"https://openalex.org/F4320331248","funder_display_name":"Shenzhen Bay Laboratory"}],"funders":[{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1954297438","https://openalex.org/W1989777815","https://openalex.org/W2002452896","https://openalex.org/W2038139711","https://openalex.org/W2051916497","https://openalex.org/W2097356092","https://openalex.org/W2114850508","https://openalex.org/W2131851312","https://openalex.org/W2143210482","https://openalex.org/W2161151688","https://openalex.org/W2201713963","https://openalex.org/W2402250173","https://openalex.org/W2785273668","https://openalex.org/W2790952361","https://openalex.org/W2906744519","https://openalex.org/W2908510526","https://openalex.org/W2922509574","https://openalex.org/W2952317511","https://openalex.org/W2954253694","https://openalex.org/W2957874522","https://openalex.org/W2968494487","https://openalex.org/W2970971581","https://openalex.org/W2991877021","https://openalex.org/W2996986155","https://openalex.org/W3010339412","https://openalex.org/W3081836708","https://openalex.org/W3105389349","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3194906223","https://openalex.org/W3216341763","https://openalex.org/W4210922059","https://openalex.org/W4221139567","https://openalex.org/W4223581484","https://openalex.org/W4224861788","https://openalex.org/W4281702815","https://openalex.org/W4286488966","https://openalex.org/W4286491305","https://openalex.org/W4295312788","https://openalex.org/W4296032638","https://openalex.org/W4297433310","https://openalex.org/W4312198153","https://openalex.org/W4318071656","https://openalex.org/W4319452608","https://openalex.org/W4324129409","https://openalex.org/W4327550249","https://openalex.org/W4385245566","https://openalex.org/W6739901393","https://openalex.org/W6757817989","https://openalex.org/W6760640297","https://openalex.org/W6765474767","https://openalex.org/W6810048072"],"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":{"Recent":[0],"advances":[1],"in":[2,66,97,113,152,162],"deep":[3,157],"learning":[4],"have":[5,24],"significantly":[6],"improved":[7],"the":[8,19,27,44,56,103,136,153,171],"ability":[9,99],"to":[10,33,102,135,165,170],"infer":[11],"protein":[12,16,75],"sequences":[13,154],"directly":[14],"from":[15,26,120],"structures":[17,142,161],"for":[18,52,78,159],"fix-backbone":[20],"design.":[21],"The":[22],"methods":[23],"evolved":[25],"early":[28],"use":[29],"of":[30,47,58,115,123,127],"multi-layer":[31],"perceptrons":[32],"convolutional":[34],"neural":[35,40],"networks,":[36],"transformers,":[37],"and":[38,86,130,143],"graph":[39,51],"networks":[41],"(GNN).":[42],"However,":[43],"conventional":[45],"approach":[46],"constructing":[48],"K-nearest-neighbors":[49],"(KNN)":[50],"GNN":[53],"has":[54],"limited":[55],"utilization":[57],"edge":[59,84],"information,":[60],"which":[61],"plays":[62],"a":[63,94,108],"critical":[64],"role":[65],"network":[67],"performance.":[68],"Here":[69],"we":[70,89],"introduced":[71],"SPIN-CGNN":[72,92],"based":[73],"on":[74],"contact":[76],"maps":[77],"nearest":[79],"neighbors.":[80],"Together":[81],"with":[82],"auxiliary":[83],"updates":[85],"selective":[87],"kernels,":[88],"found":[90],"that":[91,148],"provided":[93],"comparable":[95],"performance":[96],"refolding":[98],"by":[100,138,156],"AlphaFold2":[101],"current":[104],"state-of-the-art":[105],"techniques":[106],"but":[107],"significant":[109],"improvement":[110],"over":[111],"them":[112],"term":[114],"sequence":[116],"recovery,":[117],"perplexity,":[118],"deviation":[119],"amino-acid":[121],"compositions":[122],"native":[124,172],"sequences,":[125],"conservation":[126],"hydrophobic":[128],"positions,":[129],"low":[131,149],"complexity":[132,150],"regions,":[133],"according":[134],"test":[137],"unseen":[139],"structures,":[140],"\"hallucinated\"":[141],"diffusion":[144],"models.":[145],"Results":[146],"suggest":[147],"regions":[151],"designed":[155],"learning,":[158],"generated":[160],"particular,":[163],"remain":[164],"be":[166],"improved,":[167],"when":[168],"compared":[169],"sequences.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-30T09:04:40.226872","created_date":"2025-10-10T00:00:00"}
