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Molecular Tools: protein association rates and binding sites

Version 19.1 by richtesn on 2021/04/16 21:42

Molecular Tools: protein association rates and binding sites

This collab contains a set of tools and tutorials for exploring protein binding properties based on their electrostatics and estimation of protein-protein association rates 

Authors: Stefan Richter

What can I find here?

Please note, the corresponding usecases as jupyter notebooks will be transferred from Collaboratory 1. So far they can be found here: 
https://collab.humanbrainproject.eu/#/collab/1655/nav/362934

The corresponding guidebooks can be found here:
https://collab.humanbrainproject.eu/#/collab/1655/nav/18580

The descriptions of 

  • Tools and tutorials that describes how to:

    • simulate protein-protein association  using Brownian Dynamics (BD)  simulations (web server webSDA)
    • analyse the results of a Brownian dynamics simulation for calculating protein-protein association rate constants
    • compute protein electrostatic potential (under development)

    • compare the electrostatic potentials surrounding a set of protein  isoforms or specific regions with multipipsa (under development)

    • identify potential protein binding sites by comparing the electrostatic potentials of a set of protein isoforms (under development)

Who has access?

All EBRAINS users

Contents