{"id":"https://openalex.org/W4414382530","doi":"https://doi.org/10.1093/bib/bbaf488","title":"Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3","display_name":"Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414382530","doi":"https://doi.org/10.1093/bib/bbaf488","pmid":"https://pubmed.ncbi.nlm.nih.gov/40975836"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf488","pdf_url":null,"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://doi.org/10.1093/bib/bbaf488","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108820014","display_name":"Sen Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Sen Cao","raw_affiliation_strings":["Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China"],"raw_orcid":"https://orcid.org/0009-0009-8779-7449","affiliations":[{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101408418","display_name":"Cheng Zhu","orcid":"https://orcid.org/0009-0006-5155-1605"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Zhu","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University of Technology , Chaowang Road, Gongshu District, Hangzhou 310014 ,","College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China"],"raw_orcid":"https://orcid.org/0009-0006-5155-1605","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University of Technology , Chaowang Road, Gongshu District, Hangzhou 310014 ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101349273","display_name":"Qingyi Mao","orcid":null},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingyi Mao","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University of Technology , Chaowang Road, Gongshu District, Hangzhou 310014 ,","College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University of Technology , Chaowang Road, Gongshu District, Hangzhou 310014 ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008112425","display_name":"Jingjing Guo","orcid":"https://orcid.org/0000-0002-4632-4364"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Jingjing Guo","raw_affiliation_strings":["Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China"],"raw_orcid":"https://orcid.org/0000-0002-4632-4364","affiliations":[{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023499190","display_name":"Ning Zhu","orcid":"https://orcid.org/0000-0001-7877-8179"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":true,"raw_author_name":"Ning Zhu","raw_affiliation_strings":["Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hongliang Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":true,"raw_author_name":"Hongliang Duan","raw_affiliation_strings":["Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University , R. de Lu\u00eds Gonzaga Gomes, Macao 999078 ,","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Faculty of Applied Sciences, Macao Polytechnic University, R. de Lu\u00eds Gonzaga Gomes, Macao 999078, China","institution_ids":["https://openalex.org/I49835588"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023499190"],"corresponding_institution_ids":["https://openalex.org/I49835588"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.7225,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.84933063,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9944999814033508,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9944999814033508,"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":0.9319000244140625,"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/cyclic-peptide","display_name":"Cyclic peptide","score":0.9217000007629395},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6747000217437744},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.6545000076293945},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5764999985694885},{"id":"https://openalex.org/keywords/peptidomimetic","display_name":"Peptidomimetic","score":0.5002999901771545},{"id":"https://openalex.org/keywords/offset","display_name":"Offset (computer science)","score":0.40610000491142273}],"concepts":[{"id":"https://openalex.org/C60984968","wikidata":"https://www.wikidata.org/wiki/Q389172","display_name":"Cyclic peptide","level":3,"score":0.9217000007629395},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6747000217437744},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.6545000076293945},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5989000201225281},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5764999985694885},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.5078999996185303},{"id":"https://openalex.org/C124790011","wikidata":"https://www.wikidata.org/wiki/Q2069797","display_name":"Peptidomimetic","level":3,"score":0.5002999901771545},{"id":"https://openalex.org/C175291020","wikidata":"https://www.wikidata.org/wiki/Q1156822","display_name":"Offset (computer science)","level":2,"score":0.40610000491142273},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3903000056743622},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.36489999294281006},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3619999885559082},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.3384000062942505},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.31850001215934753},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3021000027656555},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.2815999984741211},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2759999930858612},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2563999891281128}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf488","pdf_url":null,"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:40975836","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40975836","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:europepmc.org:11259739","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12450345","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12450345","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12450345/","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf488","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf488","pdf_url":null,"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/G7287413255","display_name":null,"funder_award_id":"0151/2024/RIA2","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320323893","display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia","ror":"https://ror.org/05vna4324"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W2023272942","https://openalex.org/W2080356101","https://openalex.org/W2095947376","https://openalex.org/W2114363966","https://openalex.org/W2170564629","https://openalex.org/W2220780917","https://openalex.org/W2279263454","https://openalex.org/W2563002344","https://openalex.org/W2724823461","https://openalex.org/W2765385012","https://openalex.org/W2864915797","https://openalex.org/W2945543430","https://openalex.org/W2998881619","https://openalex.org/W3164046276","https://openalex.org/W3177828909","https://openalex.org/W3197423770","https://openalex.org/W3215749250","https://openalex.org/W4285483966","https://openalex.org/W4297138475","https://openalex.org/W4307645443","https://openalex.org/W4327550249","https://openalex.org/W4386485109","https://openalex.org/W4387865628","https://openalex.org/W4391463492","https://openalex.org/W4396229594","https://openalex.org/W4396663719","https://openalex.org/W4396721167","https://openalex.org/W4399392434","https://openalex.org/W4402913471","https://openalex.org/W4404565424","https://openalex.org/W4407603240","https://openalex.org/W4409539223","https://openalex.org/W4409621856","https://openalex.org/W4410281231","https://openalex.org/W4410552412"],"related_works":[],"abstract_inverted_index":{"Cyclic":[0,114],"peptides":[1,37],"have":[2],"emerged":[3],"as":[4],"a":[5],"research":[6],"hotspot":[7],"in":[8,11,29,154,163],"drug":[9,46],"development":[10],"recent":[12],"years":[13],"due":[14],"to":[15,85,92],"their":[16,45],"excellent":[17],"stability,":[18],"specificity,":[19],"and":[20,62,125,134,152,172,190],"cell":[21],"penetration.":[22],"However,":[23],"existing":[24,144],"computational":[25],"models":[26,145],"face":[27],"challenges":[28],"accurately":[30,86],"predicting":[31,129,164],"the":[32,56,64,72,94,104,113,130,187],"three-dimensional":[33],"structures":[34,131],"of":[35,50,59,66,132,192],"cyclic":[36,88,98,135,155,165,176,193],"containing":[38,179],"unnatural":[39],"amino":[40],"acids":[41],"(unAAs),":[42],"thereby":[43],"limiting":[44],"design.":[47],"The":[48],"release":[49],"AlphaFold":[51,105],"3":[52,106],"has":[53],"significantly":[54],"enhanced":[55,170],"modeling":[57],"capability":[58,174],"biomolecular":[60],"complexes":[61,178],"enabled":[63],"inclusion":[65],"unAAs":[67],"through":[68],"definitions":[69],"provided":[70],"by":[71,111],"Chemical":[73],"Component":[74],"Dictionary":[75],"(CCD).":[76],"Nevertheless,":[77],"its":[78,83],"training":[79],"data":[80],"reliance":[81],"limits":[82],"ability":[84],"predict":[87],"peptide":[89,99,156,166,177],"structures,":[90],"failing":[91],"meet":[93],"demand":[95],"for":[96,128,175,186],"precise":[97],"structure":[100,157],"prediction.":[101,158],"Based":[102],"on":[103],"framework,":[107],"we":[108],"developed":[109],"HighFold3":[110,120,142],"introducing":[112],"Position":[115],"Offset":[116],"Encoding":[117],"Matrix":[118],"(CycPOEM).":[119],"comprises":[121],"two":[122],"submodels:":[123],"HighFold3-Linear":[124],"HighFold3-Cyclic,":[126],"designed":[127],"linear":[133],"peptides,":[136],"respectively.":[137],"Our":[138],"results":[139],"demonstrate":[140],"that":[141],"outperforms":[143],"(HighFold,":[146],"HighFold2,":[147],"CyclicBoltz1,":[148],"NCPepFold,":[149],"CABS-flex,":[150],"ESMFold,":[151],"HelixFold)":[153],"It":[159],"achieves":[160],"atomic-level":[161],"precision":[162],"monomers":[167],"while":[168],"demonstrating":[169],"accuracy":[171],"generalization":[173],"unAAs.":[180],"This":[181],"offers":[182],"unprecedented":[183],"technical":[184],"support":[185],"structural":[188],"design":[189],"optimization":[191],"peptide-based":[194],"therapeutics.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-07-17T09:13:05.818461","created_date":"2025-10-10T00:00:00"}
