{"id":"https://openalex.org/W7203971069","doi":"https://doi.org/10.64898/2026.08.20.746104","title":"Benchmarking confidence estimation and rescoring for cyclic peptide\u2013protein complex predictions","display_name":"Benchmarking confidence estimation and rescoring for cyclic peptide\u2013protein complex predictions","publication_year":2026,"publication_date":"2026-08-21","ids":{"openalex":"https://openalex.org/W7203971069","doi":"https://doi.org/10.64898/2026.08.20.746104"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.20.746104","doi":"https://doi.org/10.64898/2026.08.20.746104","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746104","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.20.746104.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.20.746104.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5144227754","display_name":"Zhe Li","orcid":"https://orcid.org/0009-0006-8003-5845","observed_orcids":["https://orcid.org/0009-0006-8003-5845"]},"institutions":[{"id":"https://openalex.org/I4405279148","display_name":"Pharmaron (China)","ror":"https://ror.org/012qm0r35","country_code":"CN","type":"company","lineage":["https://openalex.org/I4405279148"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Li","raw_affiliation_strings":["Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China"],"raw_orcid":"https://orcid.org/0009-0006-8003-5845","affiliations":[{"raw_affiliation_string":"Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]},{"raw_affiliation_string":"In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089531615","display_name":"Ye Yuan","orcid":"https://orcid.org/0000-0001-9641-9102","observed_orcids":["https://orcid.org/0000-0001-9641-9102"]},"institutions":[{"id":"https://openalex.org/I4405279148","display_name":"Pharmaron (China)","ror":"https://ror.org/012qm0r35","country_code":"CN","type":"company","lineage":["https://openalex.org/I4405279148"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ye Yuan","raw_affiliation_strings":["Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-9641-9102","affiliations":[{"raw_affiliation_string":"Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]},{"raw_affiliation_string":"In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153575797","display_name":"Kaiqiang Hu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405279148","display_name":"Pharmaron (China)","ror":"https://ror.org/012qm0r35","country_code":"CN","type":"company","lineage":["https://openalex.org/I4405279148"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kaiqiang Hu","raw_affiliation_strings":["Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Generative Biology Group, In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]},{"raw_affiliation_string":"In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114711605","display_name":"Pengwei Pan","orcid":"https://orcid.org/0009-0009-3834-9885","observed_orcids":["https://orcid.org/0009-0009-3834-9885"]},"institutions":[{"id":"https://openalex.org/I4405279148","display_name":"Pharmaron (China)","ror":"https://ror.org/012qm0r35","country_code":"CN","type":"company","lineage":["https://openalex.org/I4405279148"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengwei Pan","raw_affiliation_strings":["In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5144236162","display_name":"Fang He","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405279148","display_name":"Pharmaron (China)","ror":"https://ror.org/012qm0r35","country_code":"CN","type":"company","lineage":["https://openalex.org/I4405279148"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fang He","raw_affiliation_strings":["In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"In Vitro Biology, Pharmaron Beijing Co., Ltd., Beijing, China","institution_ids":["https://openalex.org/I4405279148"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5153575797"],"corresponding_institution_ids":["https://openalex.org/I4405279148"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7455999851226807,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7455999851226807,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.19709999859333038,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.033399999141693115,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cyclic-peptides","display_name":"cyclic peptides","score":0.9269999861717224},{"id":"https://openalex.org/keywords/protein-peptide-complex","display_name":"protein-peptide complex","score":0.859000027179718},{"id":"https://openalex.org/keywords/confidence-estimation","display_name":"confidence estimation","score":0.746999979019165},{"id":"https://openalex.org/keywords/rescoring","display_name":"rescoring","score":0.6940000057220459},{"id":"https://openalex.org/keywords/benchmark","display_name":"benchmark","score":0.4699999988079071},{"id":"https://openalex.org/keywords/pose-ranking","display_name":"pose ranking","score":0.7269999980926514},{"id":"https://openalex.org/keywords/gradient-boosted-models","display_name":"gradient-boosted models","score":0.6129999756813049}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7904000282287598},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7078999876976013},{"id":"https://openalex.org/C52102323","wikidata":"https://www.wikidata.org/wiki/Q1671968","display_name":"Pose","level":2,"score":0.7063000202178955},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6520000100135803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6238999962806702},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5814999938011169},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.5496000051498413},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4449000060558319},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4368000030517578},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.4090000092983246},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.39640000462532043},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3499000072479248},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32089999318122864},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.28119999170303345},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.2535000145435333}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.20.746104","doi":"https://doi.org/10.64898/2026.08.20.746104","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746104","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.20.746104.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.20.746104","doi":"https://doi.org/10.64898/2026.08.20.746104","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.20.746104","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/21/2026.08.20.746104.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320324860","display_name":"Pharmaron","ror":"https://ror.org/012qm0r35"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7203971069.pdf","grobid_xml":"https://content.openalex.org/works/W7203971069.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1839137323","https://openalex.org/W2014915963","https://openalex.org/W2130086970","https://openalex.org/W2338760223","https://openalex.org/W2508425869","https://openalex.org/W2512372054","https://openalex.org/W2898210859","https://openalex.org/W2950954328","https://openalex.org/W2999615587","https://openalex.org/W3013383818","https://openalex.org/W3202105508","https://openalex.org/W3212051308","https://openalex.org/W4387865628","https://openalex.org/W4392804617","https://openalex.org/W4396721167","https://openalex.org/W4402967140","https://openalex.org/W4404565424","https://openalex.org/W4405239266","https://openalex.org/W4407603240","https://openalex.org/W4410552412","https://openalex.org/W4411463597","https://openalex.org/W4413107336","https://openalex.org/W4413802983","https://openalex.org/W4415147097","https://openalex.org/W4416815594","https://openalex.org/W4416853967","https://openalex.org/W7128427870","https://openalex.org/W7130376483","https://openalex.org/W7160545168"],"related_works":["https://openalex.org/W7220908178","https://openalex.org/W4416853967","https://openalex.org/W4386208441","https://openalex.org/W4416142729","https://openalex.org/W7208048932","https://openalex.org/W4396663719","https://openalex.org/W2996827397","https://openalex.org/W4416071068","https://openalex.org/W2479032012","https://openalex.org/W4284968387"],"abstract_inverted_index":{"Abstract":[0],"Cyclic":[1],"peptides":[2,65],"are":[3],"a":[4,28,182],"rapidly":[5],"expanding":[6],"class":[7],"of":[8,13,31,99,103,130,134,177,217],"therapeutics,":[9],"but":[10],"the":[11,85,114,147,161,174,214],"reliability":[12],"deep-learning":[14],"structure":[15],"prediction":[16,222],"for":[17,154,196,201],"cyclic":[18,219],"peptide\u2013protein":[19,220],"complexes":[20,34],"has":[21],"not":[22,151],"been":[23],"systematically":[24],"evaluated.":[25],"We":[26,158],"assembled":[27],"curated":[29],"benchmark":[30],"111":[32],"non-redundant":[33],"spanning":[35],"five":[36],"cyclization":[37],"chemistries":[38],"and":[39,45,66,87,146,223],"assessed":[40],"two":[41],"co-folding":[42],"models,":[43],"Boltz":[44],"Protenix,":[46],"each":[47],"generating":[48],"100":[49],"poses":[50,57,135],"per":[51],"target":[52,73,83],"(22,200":[53],"total).":[54],"Stratifying":[55],"all":[56],"by":[58,79,170],"complex":[59,221],"attributes,":[60],"we":[61],"found":[62],"that":[63,109,190,225],"disulfide-cyclized":[64],"small":[67],"protein":[68],"targets":[69,104],"(200":[70],"or":[71,106],"fewer":[72],"residues)":[74],"were":[75],"predicted":[76],"significantly":[77,199],"worse":[78],"both":[80,197],"tools,":[81,198],"with":[82,124,164],"size":[84],"largest":[86],"most":[88],"consistent":[89],"effect;":[90],"overall":[91],"accuracy":[92],"nevertheless":[93],"remained":[94],"high":[95,137],"(median":[96],"top-pose":[97],"DockQ":[98,144],"about":[100],"0.89,":[101],"96\u201398%":[102],"Acceptable":[105],"better),":[107],"indicating":[108],"pose":[110,125,143,149,207,211,232],"generation":[111],"is":[112],"rarely":[113],"bottleneck.":[115],"Conversely,":[116],"native":[117,162],"model":[118,138,185],"ranking":[119,139],"scores":[120],"correlated":[121],"only":[122],"moderately":[123],"quality":[126],"(Spearman":[127],"rank":[128],"correlations":[129],"0.53\u20130.66):":[131],"approximately":[132],"12%":[133],"showed":[136],"score/confidence":[140],"despite":[141],"poor":[142],"quality,":[145],"highest-quality":[148],"was":[150],"ranked":[152],"first":[153],"nearly":[155],"every":[156],"target.":[157],"therefore":[159],"augmented":[160],"score":[163],"externally":[165],"computed":[166],"interface":[167],"descriptors":[168],"normalized":[169],"chain":[171],"length,":[172],"principally":[173],"per-residue":[175],"density":[176],"inter-chain":[178],"hydrogen":[179],"bonds,":[180],"in":[181],"gradient-boosted":[183],"rescoring":[184],"evaluated":[186],"under":[187],"target-grouped":[188],"cross-validation":[189],"prevents":[191],"leakage,":[192],"improving":[193],"out-of-fold":[194],"ROC-AUC":[195],"so":[200],"Protenix.":[202],"Together,":[203],"these":[204],"findings":[205],"identify":[206],"ranking,":[208],"rather":[209],"than":[210],"generation,":[212],"as":[213],"major":[215],"limitation":[216],"current":[218],"demon-strate":[224],"complementary":[226],"structural":[227],"features":[228],"can":[229],"improve":[230],"confidence-based":[231],"selection.":[233]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-08-23T00:00:00"}