webSDA: A Web Server to Simulate Macromolecular Diffusional Association

Nucleic Acids Res. 2015 Jul 1;43(W1):W220-4. doi: 10.1093/nar/gkv335. Epub 2015 Apr 16.

Abstract

Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: 'SDA docking' to generate structures of the diffusional encounter complexes of two macromolecules, 'SDA association' to calculate bimolecular diffusional association rate constants, and 'SDA multiple molecules' to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • DNA / metabolism
  • Diffusion
  • Internet
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation*
  • Proteins / chemistry*
  • Proteins / metabolism
  • RNA / chemistry*
  • RNA / metabolism
  • Software*

Substances

  • Proteins
  • RNA
  • DNA