Prediction of the rate of formation of a protein-protein complex

Summary

This tutorial describes the use of SDA to perform Brownian dynamics simulations to predict the bimolecular diffusional association rate constant for the formation of a protein-protein complex.

 

Author(s): Neil Bruce, Gaurav Ganotra and Rebecca Wade

Author affiliations: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany

Contact email: mcmsoft@h-its.org

Version: 2.0

Submission date: Jan. 1, 2018

Last revised: May 21, 2019

Example page: Simulation of the diffusional association of barnase and barstar.

Publication: Biophysical journal 72, 1917-29.


Requirements

  1. SDA 7
  2. APBS and PDB2PQR

Instructions

The instructions for this tutorial are in the following PDF files:

The file required for the calculations are available here.