{"id":"https://openalex.org/W4391463492","doi":"https://doi.org/10.1093/bib/bbae003","title":"Structure prediction of linear and cyclic peptides using CABS-flex","display_name":"Structure prediction of linear and cyclic peptides using CABS-flex","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4391463492","doi":"https://doi.org/10.1093/bib/bbae003","pmid":"https://pubmed.ncbi.nlm.nih.gov/38305457"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae003","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae003/56542343/bbae003.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","license_id":"https://openalex.org/licenses/cc-by","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/25/2/bbae003/56542343/bbae003.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036112045","display_name":"Aleksandra E. Badaczewska-Dawid","orcid":"https://orcid.org/0000-0003-1832-4364"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]},{"id":"https://openalex.org/I2802789608","display_name":"Ames National Laboratory","ror":"https://ror.org/041m9xr71","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I173911158","https://openalex.org/I2802789608","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aleksandra Badaczewska-Dawid","raw_affiliation_strings":["Genome Informatics Facility , Office of Biotechnology, , Ames, 50011 IA,","Iowa State University , Office of Biotechnology, , Ames, 50011 IA,","Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, 50011 IA, USA"],"raw_orcid":"https://orcid.org/0000-0003-1832-4364","affiliations":[{"raw_affiliation_string":"Genome Informatics Facility , Office of Biotechnology, , Ames, 50011 IA,","institution_ids":["https://openalex.org/I2802789608"]},{"raw_affiliation_string":"Iowa State University , Office of Biotechnology, , Ames, 50011 IA,","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, 50011 IA, USA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093845620","display_name":"Karol Wr\u00f3blewski","orcid":"https://orcid.org/0000-0001-5182-1376"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Karol Wr\u00f3blewski","raw_affiliation_strings":["Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-5182-1376","affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023082406","display_name":"Mateusz Kurci\u0144ski","orcid":"https://orcid.org/0000-0002-5385-2069"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Kurcinski","raw_affiliation_strings":["Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006850152","display_name":"Sebastian Kmiecik","orcid":"https://orcid.org/0000-0001-7623-0935"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sebastian Kmiecik","raw_affiliation_strings":["Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-7623-0935","affiliations":[{"raw_affiliation_string":"Biological and Chemical Research Center , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"University of Warsaw , Faculty of Chemistry, , Pasteura 1, 02-093 Warsaw,","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006850152","https://openalex.org/A5036112045"],"corresponding_institution_ids":["https://openalex.org/I173911158","https://openalex.org/I2802789608","https://openalex.org/I4654613"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.813,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.91212356,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9994999766349792,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9994999766349792,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9993000030517578,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/flex","display_name":"FLEX","score":0.78657066822052},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7019960284233093},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.5970144271850586},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4133404791355133},{"id":"https://openalex.org/keywords/disulfide-bond","display_name":"Disulfide bond","score":0.4120945632457733},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3840750455856323},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3369305729866028},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21227431297302246},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20259660482406616}],"concepts":[{"id":"https://openalex.org/C2776252893","wikidata":"https://www.wikidata.org/wiki/Q1364836","display_name":"FLEX","level":2,"score":0.78657066822052},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7019960284233093},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.5970144271850586},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4133404791355133},{"id":"https://openalex.org/C27256138","wikidata":"https://www.wikidata.org/wiki/Q1230226","display_name":"Disulfide bond","level":2,"score":0.4120945632457733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3840750455856323},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3369305729866028},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21227431297302246},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20259660482406616},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"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/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010456","descriptor_name":"Peptides, Cyclic","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae003","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae003/56542343/bbae003.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38305457","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38305457","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:10836054","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10836054","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10836054/pdf/bbae003.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae003","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae003/56542343/bbae003.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","license_id":"https://openalex.org/licenses/cc-by","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/G25599960","display_name":null,"funder_award_id":"2020/39/B/NZ2/01301","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G7967083687","display_name":null,"funder_award_id":"2019/33/B/NZ2/02100","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391463492.pdf","grobid_xml":"https://content.openalex.org/works/W4391463492.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1607931568","https://openalex.org/W1997833081","https://openalex.org/W2008708467","https://openalex.org/W2054945796","https://openalex.org/W2059093611","https://openalex.org/W2061543974","https://openalex.org/W2101187401","https://openalex.org/W2109540804","https://openalex.org/W2125102409","https://openalex.org/W2135303325","https://openalex.org/W2139230158","https://openalex.org/W2152013549","https://openalex.org/W2162532167","https://openalex.org/W2173769259","https://openalex.org/W2323889349","https://openalex.org/W2413334978","https://openalex.org/W2739354616","https://openalex.org/W2788954552","https://openalex.org/W2800677598","https://openalex.org/W2886024678","https://openalex.org/W2891884829","https://openalex.org/W2896056828","https://openalex.org/W2905275808","https://openalex.org/W2949867299","https://openalex.org/W2982737251","https://openalex.org/W2995013727","https://openalex.org/W2998133382","https://openalex.org/W3033938335","https://openalex.org/W3039763765","https://openalex.org/W3099088600","https://openalex.org/W3127297964","https://openalex.org/W3136751755","https://openalex.org/W3177828909","https://openalex.org/W3195584572","https://openalex.org/W4211196614","https://openalex.org/W4220887281","https://openalex.org/W4225321107","https://openalex.org/W4226105311","https://openalex.org/W4281790889","https://openalex.org/W4322207749","https://openalex.org/W4327550249","https://openalex.org/W4386208441","https://openalex.org/W6810675662"],"related_works":["https://openalex.org/W4250698707","https://openalex.org/W4244545186","https://openalex.org/W4247748223","https://openalex.org/W1008394927","https://openalex.org/W183173419","https://openalex.org/W4253292776","https://openalex.org/W2483231410","https://openalex.org/W4244549413","https://openalex.org/W4239881561","https://openalex.org/W3133582567"],"abstract_inverted_index":{"The":[0,42,145],"structural":[1],"modeling":[2],"of":[3,13,20,24,37,71,77,165],"peptides":[4,73,166],"can":[5,129],"be":[6,130],"a":[7,17,29,69],"useful":[8],"aid":[9,159],"in":[10,100,149,161],"the":[11,21,34,51,61,66,83,109,126,136,150,163],"discovery":[12],"new":[14],"drugs":[15],"and":[16,39,55,74,85,97,167],"deeper":[18],"understanding":[19],"molecular":[22],"mechanisms":[23],"life.":[25],"Here":[26],"we":[27],"present":[28],"novel":[30],"multiscale":[31],"protocol":[32,43,67,127,146],"for":[33,104],"structure":[35,164],"prediction":[36,139],"linear":[38,72,122],"cyclic":[40,78],"peptides.":[41,123],"combines":[44],"two":[45,75],"main":[46],"stages:":[47],"coarse-grained":[48],"simulations":[49],"using":[50,60],"CABS-flex":[52,113,151],"standalone":[53,152],"package":[54,153],"an":[56],"all-atom":[57],"reconstruction-optimization":[58],"process":[59],"Modeller":[62],"program.":[63],"We":[64],"evaluated":[65],"on":[68],"set":[70],"sets":[76],"peptides,":[79],"with":[80,90,135,155],"cyclization":[81],"through":[82],"backbone":[84],"disulfide":[86],"bonds.":[87],"A":[88],"comparison":[89],"other":[91],"state-of-the-art":[92],"tools":[93],"(APPTEST,":[94],"PEP-FOLD,":[95],"ESMFold":[96],"AlphaFold":[98,107],"implementation":[99],"ColabFold)":[101],"shows":[102],"that":[103],"most":[105],"cases,":[106],"offers":[108],"highest":[110],"resolution.":[111],"However,":[112],"is":[114,147],"competitive,":[115],"particularly":[116],"when":[117],"it":[118],"comes":[119],"to":[120,158],"short":[121],"As":[124],"demonstrated,":[125],"performance":[128],"further":[131],"improved":[132],"by":[133],"combination":[134],"residue-residue":[137],"contact":[138],"method":[140],"or":[141],"more":[142],"efficient":[143],"scoring.":[144],"included":[148],"along":[154],"online":[156],"documentation":[157],"users":[160],"predicting":[162],"mini-proteins.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
