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.
- 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.