{"id":"https://openalex.org/W4404483445","doi":"https://doi.org/10.1371/journal.pcbi.1012609","title":"Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds","display_name":"Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds","publication_year":2024,"publication_date":"2024-11-18","ids":{"openalex":"https://openalex.org/W4404483445","doi":"https://doi.org/10.1371/journal.pcbi.1012609","pmid":"https://pubmed.ncbi.nlm.nih.gov/39556614"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1012609","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012609","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012609&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012609&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071165085","display_name":"Fei Cai","orcid":"https://orcid.org/0000-0003-2581-6682"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fei Cai","raw_affiliation_strings":["Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055684811","display_name":"Yuehua Wei","orcid":"https://orcid.org/0009-0004-2298-0975"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuehua Wei","raw_affiliation_strings":["Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072975032","display_name":"Daniel Kirchhofer","orcid":"https://orcid.org/0000-0002-0975-4402"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel Kirchhofer","raw_affiliation_strings":["Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019506521","display_name":"Andrew C. Chang","orcid":"https://orcid.org/0000-0001-9506-0425"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Andrew Chang","raw_affiliation_strings":["DeepSeq.AI, Inc., San Francisco, California United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DeepSeq.AI, Inc., San Francisco, California United States of America","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076533002","display_name":"Yingnan Zhang","orcid":"https://orcid.org/0009-0004-1268-0477"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yingnan Zhang","raw_affiliation_strings":["Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America"],"raw_orcid":"https://orcid.org/0009-0004-1268-0477","affiliations":[{"raw_affiliation_string":"Departments of Biological Chemistry, Genentech, Inc., South San Francisco, California, United States of America","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5019506521","https://openalex.org/A5076533002"],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8084,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.71196461,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"11","first_page":"e1012609","last_page":"e1012609"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991000294685364,"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":0.9976000189781189,"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/computational-biology","display_name":"Computational biology","score":0.6426607370376587},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6041699647903442},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.5684579014778137},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.48842233419418335},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.46184107661247253},{"id":"https://openalex.org/keywords/disulfide-bond","display_name":"Disulfide bond","score":0.44807860255241394},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.44715145230293274},{"id":"https://openalex.org/keywords/peptide-library","display_name":"Peptide library","score":0.41876912117004395},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37923312187194824},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.36302632093429565},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3261714577674866},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.32320505380630493},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3103085160255432},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24395135045051575},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.239772230386734},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11908721923828125}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6426607370376587},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6041699647903442},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.5684579014778137},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.48842233419418335},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.46184107661247253},{"id":"https://openalex.org/C27256138","wikidata":"https://www.wikidata.org/wiki/Q1230226","display_name":"Disulfide bond","level":2,"score":0.44807860255241394},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.44715145230293274},{"id":"https://openalex.org/C2776471321","wikidata":"https://www.wikidata.org/wiki/Q7166526","display_name":"Peptide library","level":4,"score":0.41876912117004395},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37923312187194824},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.36302632093429565},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3261714577674866},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.32320505380630493},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3103085160255432},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24395135045051575},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.239772230386734},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11908721923828125},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004220","descriptor_name":"Disulfides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1012609","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012609","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012609&type=printable","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:39556614","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39556614","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:11611271","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11611271","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11611271/pdf/pcbi.1012609.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:4d1215a122784588a2770a59d05cacae","is_oa":true,"landing_page_url":"https://doaj.org/article/4d1215a122784588a2770a59d05cacae","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 20, Iss 11, p e1012609 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1012609","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1012609","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1012609&type=printable","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":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4404483445.pdf"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1963506045","https://openalex.org/W1973897761","https://openalex.org/W1976595458","https://openalex.org/W1989527063","https://openalex.org/W1992450378","https://openalex.org/W1995390287","https://openalex.org/W1995715600","https://openalex.org/W2001313012","https://openalex.org/W2002183278","https://openalex.org/W2014050554","https://openalex.org/W2018295245","https://openalex.org/W2019096787","https://openalex.org/W2041612649","https://openalex.org/W2043409309","https://openalex.org/W2045777307","https://openalex.org/W2049277949","https://openalex.org/W2057520802","https://openalex.org/W2075489369","https://openalex.org/W2086195002","https://openalex.org/W2086959309","https://openalex.org/W2106901733","https://openalex.org/W2112035663","https://openalex.org/W2113059497","https://openalex.org/W2140237950","https://openalex.org/W2141732393","https://openalex.org/W2153456878","https://openalex.org/W2159829830","https://openalex.org/W2168080864","https://openalex.org/W2169658668","https://openalex.org/W2233221674","https://openalex.org/W2412132105","https://openalex.org/W2520613901","https://openalex.org/W2888511473","https://openalex.org/W2943688929","https://openalex.org/W2965373594","https://openalex.org/W2970863760","https://openalex.org/W2971154170","https://openalex.org/W2984894304","https://openalex.org/W3116625060","https://openalex.org/W3131932009","https://openalex.org/W3146944767","https://openalex.org/W3166142427","https://openalex.org/W3177828909","https://openalex.org/W4224939843","https://openalex.org/W4294677406","https://openalex.org/W4296032638","https://openalex.org/W4308430346","https://openalex.org/W4318071656","https://openalex.org/W4327511888","https://openalex.org/W4362560279","https://openalex.org/W4393255260","https://openalex.org/W4398201072","https://openalex.org/W6769989246"],"related_works":["https://openalex.org/W2152122195","https://openalex.org/W1492010372","https://openalex.org/W2494590260","https://openalex.org/W2610925227","https://openalex.org/W2024256163","https://openalex.org/W1988730649","https://openalex.org/W2170120749","https://openalex.org/W2067576503","https://openalex.org/W2199134476","https://openalex.org/W4372348062"],"abstract_inverted_index":{"Peptides":[0,45],"are":[1],"an":[2],"emerging":[3],"modality":[4],"for":[5,64,91,135,179,218,249,285],"developing":[6],"therapeutics":[7,67,291],"that":[8,77,96,192],"can":[9],"either":[10],"agonize":[11],"or":[12,272],"antagonize":[13],"cellular":[14],"pathways":[15],"associated":[16],"with":[17,164,189,204],"disease,":[18],"yet":[19],"peptides":[20,37,203],"often":[21],"suffer":[22],"from":[23,158,224],"poor":[24],"chemical":[25],"and":[26,39,50,115],"physical":[27],"stability,":[28],"which":[29,246],"limits":[30],"their":[31],"potential.":[32],"However,":[33,74],"naturally":[34],"occurring":[35],"disulfide-constrained":[36],"(DCPs)":[38],"de":[40,243],"novo":[41],"designed":[42,235],"Hyperstable":[43],"Constrained":[44],"(HCPs)":[46],"exhibiting":[47],"highly":[48,137],"stable":[49,113],"drug-like":[51],"scaffolds,":[52],"making":[53],"them":[54],"attractive":[55],"therapeutic":[56],"modalities.":[57],"Previously,":[58],"we":[59,75,131,152,184,234],"established":[60],"a":[61,105,112,133,155,171,208,236,242],"robust":[62],"platform":[63],"discovering":[65],"peptide":[66,89,102,238,271],"by":[68,84],"utilizing":[69],"multiple":[70],"DCPs":[71],"as":[72,229,231],"scaffolds.":[73],"realized":[76],"those":[78],"libraries":[79,140],"could":[80,281],"be":[81,121],"further":[82],"improved":[83],"considering":[85],"the":[86,101,126,143,186,200,221,225,283,286,293],"foldability":[87,145,201],"of":[88,146,202,211,289],"scaffolds":[90,103],"library":[92,128,239,258,276],"design.":[93,129],"We":[94],"hypothesized":[95],"specific":[97],"sequence":[98],"patterns":[99],"within":[100],"played":[104],"crucial":[106],"role":[107],"in":[108,125,292],"spontaneous":[109],"folding":[110,251,264],"into":[111],"topology,":[114],"thus,":[116],"these":[117],"sequences":[118,212],"should":[119],"not":[120,197],"subject":[122],"to":[123,169,196],"randomization":[124],"original":[127],"Therefore,":[130],"developed":[132],"method":[134],"designing":[136],"diverse":[138],"DCP":[139],"while":[141],"preserving":[142],"inherent":[144],"each":[147],"scaffold.":[148],"To":[149],"achieve":[150],"this,":[151],"first":[153],"generated":[154],"large-scale":[156],"dataset":[157],"yeast":[159],"surface":[160],"display":[161],"(YSD)":[162],"combined":[163],"shotgun":[165],"alanine":[166,226],"scan":[167],"experiments":[168],"train":[170],"machine-learning":[172],"(ML)":[173],"model":[174,188],"based":[175,240],"on":[176,241],"techniques":[177],"used":[178],"natural":[180],"language":[181],"understanding.":[182],"Then":[183],"validated":[185],"ML":[187],"experiments,":[190],"showing":[191],"it":[193],"is":[194],"able":[195],"only":[198],"predict":[199],"high":[205],"accuracy":[206],"across":[207],"broad":[209],"range":[210],"but":[213],"also":[214],"pinpoint":[215],"residues":[216],"critical":[217],"foldability.":[219],"Using":[220],"insights":[222],"gained":[223],"scanning":[227],"experiment":[228],"well":[230],"prediction":[232],"model,":[233],"new":[237],"novo-designed":[244],"HCP,":[245],"was":[247],"optimized":[248],"enhanced":[250],"efficiency.":[252],"Subsequent":[253],"panning":[254],"trials":[255],"using":[256],"this":[257,268],"yielded":[259],"promising":[260],"hits":[261],"having":[262],"good":[263],"properties.":[265],"In":[266],"summary,":[267],"work":[269],"advances":[270],"small":[273],"protein":[274],"domain":[275],"design":[277],"practices.":[278],"These":[279],"findings":[280],"pave":[282],"way":[284],"efficient":[287],"development":[288],"peptide-based":[290],"future.":[294]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}
