Coarse-grain modelling of DNA
This page summarises (in reverse chronological order) inter-related group projects related to our coarse-grain modelling of DNA.
Using cgDNA+ model to compute sequence-dependent shapes for DNA minicircles
Results of discrete cgDNA+ energy minimization to find DNA minicircle equilibrium configuration.
- Beaud, M. "Using cgDNA+ model to compute sequence-dependent shapes for DNA minicircles". Master thesis. EPFL, 2021.
- Further material is available at this supplementary webpage.
cgDNA+: a sequence-dependent rigid-base and rigid-phosphate model of DNA
Description of a sequence-dependent coarse-grain model with explicit description of bases and phosphate groups trained from state-of-the-art Molecular dynamics simulations.
cgDNAweb: a web based viewer for the cgDNA model
Given the input sequence, and a selected parameter set, you can view the ground state of the DNA in the '3D View' or in the '2D Plots'. http://cgdnaweb.epfl.ch
Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA
A description of a method based on maximum absolute entropy principle for fitting an observed matrix of covariances for the cgDNA coarse grain model. The cgDNAparamset2 described in the article is available for download.
Sequence-dependent persistence lengths of DNA
A study of DNA persistence lengths using a code cgDNAmc to run Monte Carlo simulations within the cgDNA coarse grain model. The cgDNAmc simulation code, as well as the cgDNAparamset2 used in the simulations are available for download.
µABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.
Microsecond time-scale MD simulations of the ABC oligomers used to parameterise the cgDNA coarse grain model.
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.
cgDNA package of Matlab™ scripts for reconstructing shapes, stiffnesses and free energies of rigid-base DNA. Presented in:
A sequence-dependent rigid-base model of DNA
The original description of the cgDNA sequence-dependent rigid-base model of DNA including parameter estimation from Molecular Dynamics simulations. Example reconstructions for sequences from the training set and three sequences with point mutations.
- O. Gonzalez, D. Petkevičiūtė, and J.H. Maddocks. A sequence-dependent rigid-base model of DNA. J. Chem. Phys. 138 (5), 2013; doi: 10.1063/1.4789411. (PDF of the article and its supplementary material)
- D. Petkevičiūtė, PhD thesis #5520, EPFL 2012.
- Further material available at this supplementary webpage.