{"id":"https://openalex.org/W4406197632","doi":"https://doi.org/10.1093/bib/bbae714","title":"<i>cyclicpeptide</i>: a Python package for cyclic peptide drug design","display_name":"<i>cyclicpeptide</i>: a Python package for cyclic peptide drug design","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406197632","doi":"https://doi.org/10.1093/bib/bbae714","pmid":"https://pubmed.ncbi.nlm.nih.gov/39783893"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae714","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae714","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae714/61389377/bbae714.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/26/1/bbae714/61389377/bbae714.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001914104","display_name":"Yang Liu","orcid":"https://orcid.org/0000-0002-3889-9707"},"institutions":[{"id":"https://openalex.org/I4210126592","display_name":"National Clinical Research","ror":"https://ror.org/03ddkvp86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210126592"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Liu Yang","raw_affiliation_strings":["National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,"],"affiliations":[{"raw_affiliation_string":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","institution_ids":["https://openalex.org/I4210126592","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020151398","display_name":"Suqi Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126592","display_name":"National Clinical Research","ror":"https://ror.org/03ddkvp86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210126592"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Suqi Cao","raw_affiliation_strings":["National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,"],"affiliations":[{"raw_affiliation_string":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","institution_ids":["https://openalex.org/I4210126592","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085119058","display_name":"Lei Liu","orcid":"https://orcid.org/0000-0002-9378-6342"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I4210132741","display_name":"Shanghai Tenth People's Hospital","ror":"https://ror.org/03vjkf643","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210132741"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Liu","raw_affiliation_strings":["Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,"],"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,","institution_ids":["https://openalex.org/I4210132741","https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100749287","display_name":"Ruixin Zhu","orcid":"https://orcid.org/0000-0002-5070-6453"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I4210132741","display_name":"Shanghai Tenth People's Hospital","ror":"https://ror.org/03vjkf643","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210132741"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruixin Zhu","raw_affiliation_strings":["Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,"],"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Shanghai Tenth People\u2019s Hospital, School of Life Sciences and Technology, Tongji University , 1239 Siping Road, Shanghai 200072 ,","institution_ids":["https://openalex.org/I4210132741","https://openalex.org/I116953780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022846353","display_name":"Dingfeng Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126592","display_name":"National Clinical Research","ror":"https://ror.org/03ddkvp86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210126592"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Dingfeng Wu","raw_affiliation_strings":["National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,"],"affiliations":[{"raw_affiliation_string":"National Center, Children\u2019s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health , 3333 Binsheng Road, Hangzhou 310052 ,","institution_ids":["https://openalex.org/I4210126592","https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5001914104"],"corresponding_institution_ids":["https://openalex.org/I4210126592","https://openalex.org/I76130692"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.3738,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.81703868,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","issue":"1","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":0.9998000264167786,"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/T10911","display_name":"Chemical Synthesis and Analysis","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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9979000091552734,"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":0.9976000189781189,"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":0.842942476272583},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7565880417823792},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.59219890832901},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5640606880187988},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34475576877593994},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33479249477386475},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.32256579399108887},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2595676779747009},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24584224820137024},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12662366032600403},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11636480689048767}],"concepts":[{"id":"https://openalex.org/C60984968","wikidata":"https://www.wikidata.org/wiki/Q389172","display_name":"Cyclic peptide","level":3,"score":0.842942476272583},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7565880417823792},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.59219890832901},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5640606880187988},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34475576877593994},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33479249477386475},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.32256579399108887},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2595676779747009},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24584224820137024},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12662366032600403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11636480689048767}],"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":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":"Q000494","qualifier_name":"pharmacology","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":"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae714","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae714","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae714/61389377/bbae714.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:39783893","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39783893","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:11713021","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11713021","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11713021/pdf/bbae714.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/bbae714","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae714","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae714/61389377/bbae714.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/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3135901300","display_name":null,"funder_award_id":"82304351","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4364701651","display_name":null,"funder_award_id":"32200529","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406197632.pdf","grobid_xml":"https://content.openalex.org/works/W4406197632.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W2114850508","https://openalex.org/W2207769928","https://openalex.org/W2417990257","https://openalex.org/W2889885924","https://openalex.org/W2920795827","https://openalex.org/W2937307539","https://openalex.org/W2960787887","https://openalex.org/W3088499242","https://openalex.org/W3094286125","https://openalex.org/W3097358871","https://openalex.org/W3106304714","https://openalex.org/W3112951420","https://openalex.org/W3118410948","https://openalex.org/W3163880690","https://openalex.org/W3168436232","https://openalex.org/W4226280034","https://openalex.org/W4283024559","https://openalex.org/W4294816770","https://openalex.org/W4294982900","https://openalex.org/W4297183296","https://openalex.org/W4312224766","https://openalex.org/W4322207749","https://openalex.org/W4323657947","https://openalex.org/W4382631326","https://openalex.org/W4384563047","https://openalex.org/W4385716229","https://openalex.org/W4386636681","https://openalex.org/W4387107536","https://openalex.org/W4388891970","https://openalex.org/W4389379414","https://openalex.org/W4389702533","https://openalex.org/W4391070161","https://openalex.org/W4396229594","https://openalex.org/W4399258661"],"related_works":["https://openalex.org/W4406161738","https://openalex.org/W2589939877","https://openalex.org/W2081553665","https://openalex.org/W2892113376","https://openalex.org/W2030585732","https://openalex.org/W3012180934","https://openalex.org/W2078683866","https://openalex.org/W2063421454","https://openalex.org/W4205708008","https://openalex.org/W2958691256"],"abstract_inverted_index":{"The":[0],"unique":[1],"cyclic":[2,5,28,57,78,89,118,129],"structure":[3,80],"of":[4,24,100,110,117,128],"peptides":[6,119],"grants":[7],"them":[8,14],"remarkable":[9],"stability":[10],"and":[11,70,76,81,92,94,104],"bioactivity,":[12],"making":[13],"powerful":[15],"candidates":[16],"for":[17,27,56,88],"treating":[18],"various":[19],"diseases.":[20],"However,":[21],"the":[22,98,115,126],"lack":[23],"standardized":[25,64],"tools":[26,65,111],"peptide":[29,58,79],"data":[30],"has":[31],"hindered":[32],"their":[33,101],"potential":[34,105],"in":[35],"today's":[36],"artificial":[37],"intelligence-driven":[38],"efficient":[39],"drug":[40,59,122],"design":[41],"landscape.":[42],"To":[43],"bridge":[44],"this":[45],"gap,":[46],"here":[47],"we":[48],"introduce":[49],"a":[50],"Python":[51],"package":[52,62],"named":[53],"cyclicpeptide":[54],"specifically":[55],"design.":[60],"This":[61,107],"provides":[63],"such":[66],"as":[67],"Structure2Sequence,":[68],"Sequence2Structure,":[69],"format":[71],"transformation":[72],"to":[73,96,113],"process,":[74],"convert,":[75],"standardize":[77],"sequence":[82],"data.":[83],"Additionally,":[84],"it":[85],"includes":[86],"GraphAlignment":[87],"peptide-specific":[90],"alignment":[91],"search":[93],"PropertyAnalysis":[95],"enhance":[97],"understanding":[99],"drug-like":[102],"properties":[103],"applications.":[106],"comprehensive":[108],"suite":[109],"aims":[112],"streamline":[114],"integration":[116],"into":[120],"modern":[121],"discovery":[123],"pipelines,":[124],"accelerating":[125],"development":[127],"peptide-based":[130],"therapeutics.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-01-09T00:00:00"}