cgDNA - a package of Matlab™ scripts for predicting shapes, stiffnesses and free energy differences of rigid-base DNA
The cgDNA package allows efficient construction of the free-energy minimising shape and associated stiffness for a DNA sequence of any length. Free energy differences between different configurations of a DNA molecule can then be computed. Shapes can be input and output in coordinates defined by the program Curves+. cgDNA can also output atomistic coordinates of DNA bases in PDB format, which can then be used to obtain shape parameters in other conventions (for example those of 3DNA). The description of the package and the assessment of its performance by comparing DNA shape predictions with MD simulation, NMR and crystallographic data can be found in:
- D. Petkevičiūtė, M. Pasi, O. Gonzalez and J.H. Maddocks. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA. Nucleic Acids Research 2014; doi: 10.1093/nar/gku825. (♦)
The cgDNA package implements the cgDNA coarse-grain sequence-dependent rigid-base model of DNA with a parameter set trained on molecular dynamics simulations, described in: O. Gonzalez, D. Petkevičiūtė, and J.H. Maddocks. A sequence-dependent rigid-base model of DNA. J. Chem. Phys. 138 (5), 2013. (♦♦)If you use the cgDNA package, please cite (♦) for the software and (♦♦) for the original description of the model.
The cgDNA package was tested on Matlab™ versions 7.7 (R2008b), 8.0 (R2012b), 8.2 (R2013b), and GNU Octave, versions 3.6.2 and 3.6.4 (free download of GNU Octave is available from http://www.gnu.org/software/octave).