webSDA: a web server to simulate macromolecular diffusional association

Abstract

Macromolecular interactions play a crucial role in bi-ological systems. Simulation of diffusional associa-tion (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macro-molecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolec-ular association and encounter complex formation, to compute association rate constants, and to in-vestigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facili-tates and automates the use of the SDA software, and offers user-friendly visualization of results. web-SDA currently has three modules: ‘SDA docking’ to generate structures of the diffusional encounter complexes of two macromolecules, ‘SDA associa-tion ’ to calculate bimolecular diffusional association rate constants, and ‘SDA multiple molecules ’ to sim-ulate the diffusive motion of hundreds of macro-molecules. webSDA is freely available to all users and there is no login requirement. webSDA is avail-able a