# 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

**ŵ**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:

- O. Gonzalez, D. Petkevičiūtė, and J.H. Maddocks. A sequence-dependent rigid-base model of DNA. J. Chem. Phys. 138 (5), 2013. (journal page) (♦) (Local copy of the pdf of the article and its supplementary material).
- D. Petkevičiūtė, PhD thesis, EPFL 2012.

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