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.

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:

R. Lavery, K. Zakrzewska, D. Beveridge, T. Bishop, D. Case, T. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, and J. Sponer. A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res., 38(1):299-313, 2010.

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