REDUX

Torsion angle Monte Carlo protein molecular simulations

The above figure shows an oligopeptide model using the unified residue construction of REDUX. The model includes,

• a CA atom
• a single pseudo atom side chain with radius proportional to side chain size
• a backbone pseudo hydrogen bond site (of zero interaction radius) between each pair of CA atoms

REDUX was written in Python by P.J. Fleming and is designed for more efficient exploration of conformational space compared to all atom peptide models.

I have found it useful for converting an extended polypeptide to a compact "molten" globule form of the protein.

It could also be used to create an ensemble of excluded volume peptide conformations.

The "force field" terms can be iteratively altered to control the final characteristics of the polypeptide ensemble. These terms include:

• Soft debump (V = Eps,i,j[(Sigma,i,j/ri,j)**12],
• Residue specific pairwise contact
• Radius of gyration (Rg) confinement
• Backbone hydrogen bond strength
• Backbone mesostate distribution (directed Ramachandran plot distributions)

Download the distribution as a tarred and gzipped archive file.
A userguide in PDF format is available.
The userguide is a minimalist getting started document. If you would like more information about REDUX please email pat.fleming_at_jhu.edu.