# Coarse-grain modelling of DNA

This page summarises (in reverse chronological order) inter-related group projects related to our coarse-grain modelling of DNA.

### Computations with the cgDNA+ coarse-grain model of DNA

Results of the master semester project on computing minicircle shapes and helicoidal configurations.

- Federica, P. "Computations with the cgDNA+ coarse-grain model of DNA". Master Semester Project. EPFL, 2022.
- Further material on the compuattion of minicircle shapes is available at this supplementary webpage .
- Further material on the computation of uniform helicoidal configurations is available at this supplementary webpage.

### 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.