{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T13:07:01Z","timestamp":1774271221043,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,11,30]],"date-time":"2025-11-30T00:00:00Z","timestamp":1764460800000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"\u2018Pioneer\u2019 and \u2018Leading Goose\u2019 R&D Program of Zhejiang","award":["2025C01117"],"award-info":[{"award-number":["2025C01117"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["22220102001"],"award-info":[{"award-number":["22220102001"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82204210"],"award-info":[{"award-number":["82204210"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82204279"],"award-info":[{"award-number":["82204279"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["226\u20132022-00220"],"award-info":[{"award-number":["226\u20132022-00220"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2025BSSXM20"],"award-info":[{"award-number":["2025BSSXM20"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cyclic peptides represent a highly promising class of biopharmaceutical scaffolds. The screening of cyclic peptides against protein targets can be greatly facilitated using computational approaches, especially molecular docking. However, it remains a crucial challenge to accurately predict protein\u2013cyclic peptide (P\u2013cp) interactions employing scoring functions of molecular docking. End-point approaches, such as molecular mechanics generalized Born surface area (MM\/GBSA) and molecular mechanics Poisson\u2013Boltzmann surface area (MM\/PBSA), provide theoretically more robust frameworks than conventional scoring functions, but their reliability in predicting binding affinities and discriminating native-like binding poses for P\u2013cp complexes remains poorly quantified. Herein, we comprehensively assessed the predictive abilities of MM\/PBSA(GBSA) in scoring binding affinities of P\u2013cp complexes and re-ranking their binding poses. The binding affinity scoring ability of MM\/PBSA(GBSA) was assessed on a carefully curated dataset consisting of 50 complexes involving P\u2013cp binding affinities, and their re-ranking capability was evaluated on another dataset consisting of the decoys of 81 P\u2013cp complexes. Based on these assessments, we proposed a two-step workflow for predicting P\u2013cp binding affinities. First, we employed the assessed optimal re-ranking method to select the top-1 binding pose; second, we estimated the binding affinity based on the selected top-1 pose using the assessed optimal scoring method. Our proposed workflow, which requires only 3\u00a0s for each prediction, achieves binding affinity predictions with a Rp of \u22120.732 when compared to experimental values, which is twice as high as that of AutoDock CrankPep (Rp\u00a0=\u2009\u22120.316). This study emphasizes the necessity of using fine-tuned MM\/PBSA(GBSA) methods for predicting P\u2013cp interactions.<\/jats:p>","DOI":"10.1093\/bib\/bbaf632","type":"journal-article","created":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T12:34:04Z","timestamp":1762778044000},"source":"Crossref","is-referenced-by-count":3,"title":["Improving the predictive performance of binding affinities and poses for protein\u2013cyclic peptide complexes through fine-tuned MM\/PBSA(GBSA)-based methods"],"prefix":"10.1093","volume":"26","author":[{"given":"Huifeng","family":"Zhao","sequence":"first","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]},{"name":"Hangzhou Carbonsilicon AI Technology Co., Ltd , Hangzhou, Zhejiang 310018 ,","place":["China"]}]},{"given":"Jianxiang","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]},{"name":"Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine , Shanghai 200025 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8476-7548","authenticated-orcid":false,"given":"Gaoqi","family":"Weng","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]}]},{"given":"Dejun","family":"Jiang","sequence":"additional","affiliation":[{"name":"Xiangya School of Pharmaceutical Sciences, Central South University , Changsha, Hunan 410004 ,","place":["China"]}]},{"given":"Renling","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0999-8802","authenticated-orcid":false,"given":"Yu","family":"Kang","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]},{"name":"Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development , Jinhua, Zhejiang 321016 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7227-2580","authenticated-orcid":false,"given":"Tingjun","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Pharmaceutical Sciences, Zhejiang University , Yuhangtang Road 866, Hangzhou, Zhejiang 310058 ,","place":["China"]},{"name":"Zhejiang Provincial Key Laboratory for Intelligent Drug Discovery and Development , Jinhua, Zhejiang 321016 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,11,30]]},"reference":[{"key":"2025113002034210400_ref1","doi-asserted-by":"publisher","first-page":"e202308251","DOI":"10.1002\/anie.202308251","article-title":"Cyclic peptides for drug development","volume":"63","author":"Ji","year":"2024","journal-title":"Angew Chem Int Ed"},{"key":"2025113002034210400_ref2","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.cbpa.2017.04.012","article-title":"Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets","volume":"38","author":"Naylor","year":"2017","journal-title":"Curr Opin Chem Biol"},{"key":"2025113002034210400_ref3","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1002\/med.21639","article-title":"A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies","volume":"40","author":"Jing","year":"2020","journal-title":"Med Res 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