Molecular docking is an essential computational tool in structure-based drug discovery and the investigation of the molecular mechanisms underlying biological processes. Despite the development of many molecular docking programs for various systems, a universal tool that can accurately dock ligands across multiple system types remains elusive. Meeting the need, we developed XDock, a versatile docking framework built for both protein-ligand and nucleic acid-ligand interactions. XDock efficiently accounts for ligand flexibility by docking multiple conformations of a ligand and flexibly refining the final binding poses. It utilizes a distance geometric method for ligand sampling and leverages our knowledge-based scoring functions for assessing protein-ligand and nucleic acid-ligand interactions. XDock has undergone extensive validations on diverse benchmarks of protein-ligand and nucleic acid-ligand complexes and was compared with six other docking methods, including DOCK 6, AutoDock Vina, PLANTS, LeDock, rDock, and RLDock. In addition, XDock is also computationally efficient and on average can dock a ligand within 1 min.

中文翻译：

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XDock：一种用于模拟蛋白质-配体和核酸-配体相互作用的通用对接方法。


分子对接是基于结构的药物发现和研究生物过程背后的分子机制中必不可少的计算工具。尽管为各种系统开发了许多分子对接程序，但能够在多种系统类型中准确对接配体的通用工具仍然难以捉摸。为了满足这一需求，我们开发了 XDock，这是一种为蛋白质-配体和核酸-配体相互作用而构建的多功能对接框架。XDock 通过对接配体的多个构象并灵活地优化最终的结合姿势，有效地考虑了配体的灵活性。它利用距离几何方法进行配体采样，并利用我们基于知识的评分函数来评估蛋白质-配体和核酸-配体相互作用。XDock 已针对蛋白质-配体和核酸-配体复合物的不同基准进行了广泛的验证，并与其他六种对接方法进行了比较，包括 DOCK 6、AutoDock Vina、PLANTS、LeDock、rDock 和 RLDock。此外，XDock 的计算效率也很高，平均可以在 1 分钟内对接配体。