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Structural information of a peptide is essential to understand its interaction with its target. However, due to the high flexibility of peptides, it is difficult to sample the near-native conformations of a peptide. Here, we have developed an extended version of our MODPEP approach, named MODPEP2.0, to fast generate the conformations of cyclic peptides formed by a disulfide bond. MODPEP2.0 builds the three-dimensional (3D) structures of a cyclic peptide from scratch by assembling amino acids one by one onto the cyclic fragment based on the constructed rotamer and cyclic backbone libraries. Being tested on a data set of 193 diverse cyclic peptides, MODPEP2.0 obtained a considerable advantage in both accuracy and computational efficiency, compared with other sampling algorithms including PEP-FOLD, ETKDG, and modified ETKDG (mETKDG). MODPEP2.0 achieved a high sampling accuracy with an average C<jats:inline-formula><jats:alternatives><jats:tex-math>$$\\alpha$$<\/jats:tex-math><mml:math xmlns:mml=\"http:\/\/www.w3.org\/1998\/Math\/MathML\">\n                  <mml:mi>\u03b1<\/mml:mi>\n                <\/mml:math><\/jats:alternatives><\/jats:inline-formula> RMSD of 2.20 \u00c5 and 1.66 \u00c5 when 10 and 100 conformations were considered, respectively, compared with 3.41 \u00c5 and 2.62 \u00c5 for PEP-FOLD, 3.44 \u00c5 and 3.16 \u00c5 for ETKDG, 3.09 \u00c5 and 2.72 \u00c5 for mETKDG. MODPEP2.0 also reproduced experimental peptide structures for 81.35% of the test cases when an ensemble of 100 conformations were considered, compared with 54.95%, 37.50% and 50.00% for PEP-FOLD, ETKDG, and mETKDG. MODPEP2.0 is computationally efficient and can generate 100 peptide conformations in one second. MODPEP2.0 will be useful in sampling cyclic peptide structures and modeling related protein-peptide interactions, facilitating the development of cyclic peptide drugs.<\/jats:p>","DOI":"10.1186\/s13321-022-00605-8","type":"journal-article","created":{"date-parts":[[2022,5,3]],"date-time":"2022-05-03T12:03:12Z","timestamp":1651579392000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond"],"prefix":"10.1186","volume":"14","author":[{"given":"Huanyu","family":"Tao","sequence":"first","affiliation":[]},{"given":"Qilong","family":"Wu","sequence":"additional","affiliation":[]},{"given":"Xuejun","family":"Zhao","sequence":"additional","affiliation":[]},{"given":"Peicong","family":"Lin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4209-4565","authenticated-orcid":false,"given":"Sheng-You","family":"Huang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,5,3]]},"reference":[{"issue":"10","key":"605_CR1","doi-asserted-by":"publisher","first-page":"2700","DOI":"10.1016\/j.bmc.2017.06.052","volume":"26","author":"JL Lau","year":"2018","unstructured":"Lau JL, Dunn MK (2018) Therapeutic peptides: historical perspectives, current development trends, and future directions. 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