Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock

IF 5.5 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2025-08-24 DOI:10.1021/acs.jctc.5c00995

Mateusz Zalewski, Aleksandra Badaczewska-Dawid and Sebastian Kmiecik*,

引用次数: 0

Abstract

Cyclic peptides are promising therapeutics, but their flexible docking remains challenging. We present a protocol based on the well-established CABS-dock method, enhanced with cyclic restraints and Rosetta refinement. The approach was evaluated on 38 benchmark complexes previously used in other docking method studies. While selecting the truly best model remains difficult, near-native solutions are frequently sampled. CABS-dock offers global, unbiased docking without prior binding site knowledge, making it valuable for pose generation, structural ensemble modeling, and integration into AI-driven peptide–protein docking workflows.

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利用cab -对接技术实现环肽与蛋白质的柔性对接。

环肽是一种很有前途的治疗方法，但其灵活对接仍然具有挑战性。我们提出了一种基于完善的CABS-dock方法的协议，增强了循环约束和Rosetta细化。该方法在其他对接方法研究中使用的38个基准配合物上进行了评估。虽然选择真正最好的模型仍然很困难，但接近原生的解决方案经常被采样。CABS-dock提供全局、无偏对接，无需事先了解结合位点，这对于姿态生成、结构集成建模以及集成到人工智能驱动的肽蛋白对接工作流程非常有价值。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.