Design construct renaming and input pdb files.

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform (RPX) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.经计算设计的多亚基组装体在诸多应用领域中展现出可观的应用潜力，其中涵盖新一代强效疫苗研发。此类组装体的主流制备途径之一，是将环状寡聚体进行不依赖序列的刚体对接，以构建具有点群或晶格对称性的结构。当前用于此类组装体对接与设计的方法均针对特定对称性类别开发，难以适配新型应用场景的改造需求。本文介绍了RPXDock——一款快速、灵活且模块化的软件工具包，可实现跨多种对称结构的不依赖序列的刚体蛋白质对接，且易于定制以支持后续开发。RPXDock采用高效的分层搜索策略与残基对变换（residue-pair transform, RPX）打分方法，可快速遍历多维对接空间。本文详细阐述了该软件的架构，提供了实用的使用指南，并介绍了其内置的各类功能模块，包括多种打分函数与筛选工具，可用于引导并优化对接结果以得到目标构型。