Coarse Grained Models

Exploring the landscape of large scale conformational changes such as protein folding at atomic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed(1).Coarse-grained representations combined with enhanced computer power allow the simulation of system of biologically relevant size(submicrometric) and time scale(us or ms)(2).

The beads model is a model based on a united-atom representation of the amino acid(involving one to six interaction centers).


​​<1> Elastic network models

The system is represented by a network of beads connected by elastic springs,usually one bead per amino acid.

<2> G\bar{o}-like models

The G\bar{o} model was propsed specifically for the simulation of protein folding. In the original version, the protein is represented as a chain of one-bead amino acids whose structure is biased toward the native configuration by means of simple attractive and repulsive non-bonded interaction between beads.

In the G\bar{o} model, amino acids are represented by point particles, or beads, which are located at the positions of the Ca atoms. Consecutive beads in the chain are tethered by an anharmonic potential: {V}_{BB}=\sum_{i=1}^{N-1}{U}_{BB}({d}_{i}) , where {d}_{i} is the distance between beads i and i+1,


The use of an advanced sampling method like replica exchange can be used to rapidly explore conformational space.

Both ENM and G\bar{o} model depend on reference configuration which makes them weakly transferable to general dynamics studies.




1. Insights from Coarse-Grained Go Models for Protein Folding and Dynamics.

2.Coarse-grained models for proteins