BILBOMD: Modeling flexible macromolecular systems using molecular dynamics and genetic algorithms

About a year ago I started a project with Michal Hammel from the Lawrence Berkeley National Lab on using a genetic algorithm for modeling flexible macromolecular systems (more specifically, the focus was on large proteins of over 900 amino acids).

To make the long story short, some proteins do not have rigid structure, but their structure changes over time. These proteins would typically contain several rigid modules, which are connected with flexible linkers. The goal of this project is to find out how the structure changes over time based on experimental results from solution-based SAXS (small angle X-ray scattering) and theoretical conformations computed with molecular dynamics (MD) simulations.

The basic idea of this approach called BILBOMD follows:
1. Compute experimental scattering profile using solution-based SAXS.
2. Compute a large number (1k to 10k) of potential conformations using molecular dynamics simulation.
3. Use a genetic algorithm to select a subset of conformations explaining the experimental scattering profile best.

The results are promising and we’re working on making these results even better and more useful.

A web page dedicated to this project can be found here.

One comment on “BILBOMD: Modeling flexible macromolecular systems using molecular dynamics and genetic algorithms

  1. Marcelo on said:

    Hi, Martin!

    Thank you very much for your comment and explanation concerning the EA you used. :)

    See You!

    Marcelo