Section: New Software and Platforms

Protein-Marshmallow

Keywords: Coarse-Grained Representation

Scientific Description

A Protein-protein interaction may be considered in terms of physical interaction between two deformable objects. The description at the atomic level of such complex objects is beginning to be feasible by MD simulations, but this requires the use of petaflop machines which are out of reach of most laboratories.

Functional Description

The Protein-Marshmallow program represents the surface of a protein as “coarse grained” 3D triangle mesh. In this mesh, each triangle is colored according to some biological property. In this way, a large complex object may be represented by a much smaller number of samples in a 3D mesh. The Marshmallow program describes deformations of such meshes under the influence of an external force field to simulate the strains that one object may undergo over time due to the interaction with another one.

• Contact: Bernard Maigret