A sequence-dependent rigid-base model of DNA: a best-fit parameter set and examples.

In our coarse-grain rigid base model of DNA, to every DNA sequence we associate a quadratic potential (free energy) of the form

U = 1/2(w - ŵ)·K(w - ŵ)+Û.

A dimer-dependent best-fit parameter set P* allows us to reconstruct the stiffness matrix K and the shape vector for any given DNA sequence of any length.

The full parameter set P*, as well as Matlab™ scripts for stiffness and shape reconstructions, can be downloaded from this webpage. Moreover, there are some plots of reconstructed parameters, compared to the ones directly estimated from the MD simulations.

A description of the model, the parameter extraction procedure and the parameter set can be found in:

The main part of the Molecular Dynamics data used for the model parameter estimation was produced by the ABC consortium. The MD simulation protocol can be found in:

If you use data, scripts or figures from this webpage, please cite (♦).