BioExcel Webinar #23 - MC_DNA: A web server for the detailed study of the structure and dynamics of DNA and chromatin fibers

MC_DNA is a new web tool for the three-dimensional simulation of free DNA and medium-sized chromatin fibers. The program implements a Monte Carlo algorithm based on a mesoscopic model, using a tetramer-dependent base-pair step model fitted to reproduce parmbsc1 atomistic molecular dynamics (MD) simulations. The Monte Carlo ensembles can be projected to the atomistic level of resolution and processed to obtain quasi-time-dependent trajectories. The method provides ensembles of quality comparable to those obtained from atomistic MD, but at a tiny fraction of the computational cost, allowing to study systems much larger than those explored by atomistic MD. The trajectories (at atomistic or bp resolution levels) can be downloaded and/or subjected to a large variety of analysis in the server. All the tools are implemented in a friendly web interface where the user needs to specify only the DNA sequence, its topology (linear or circular) and whether the DNA fiber is free or protein-bound. In the case of protein(s) bound to the DNA, the user needs to provide also the PDB code of the protein(s) and the position(s) of DNA where the protein(s) is(are) placed. Alternatively, the user can scan for the region(s) of DNA which are better shaped to adopt the bioactive conformation. The tool uses state-of-the-art technologies such as i) Open Nebula cloud infrastructure with virtual machines deployed on demand for computations, ii) WebGL-programmed NGL molecular viewer and the javascript plotly library for interactive plots, and iii) noSQL-MongoDB for storage. The server is accessible at http://mmb.irbbarcelona.org/MCDNA/. In the webinar the theory behind the simulation will be discussed and possible inputs for simulations will be pointed out. Afterwards, all the individual analysis tools will be explained and illustrated with examples