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
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.
This is the second BioExcel – Multiscale Complex Genomics joint webinar.
MCDNA is integrated in the Multiscale Complex Genomics Virtual Research Environment (MuG-VRE)
Jürgen Walther, IRB Barcelona
Jürgen Walther obtained his B.Sc. degree at the University of Würzburg (Germany) in Physics. His final degree work was done in Astrophysics with the name “Hard X-ray properties of Water Maser Galaxies”. He did his master degree at the University of Texas at Austin (USA) in Physics with specialization in Biophysics. There he was working on refining a microscope technique involving light microscopy, TIRF fluorescence and optical trapping to visualize the movement of molecular motors walking along microtubules. He is now working as a PhD student in the Molecular modeling and bioinformatics laboratory of Modesto Orozco at the Institute for Research in Biomedicine Barcelona (Spain). His main focus is to bridge known information of free DNA and of chromatin maintaining a high level of resolution in the theoretical models used. To achieve this goal the application MC_DNA was developed and integrated into a webserver (http://mmb.irbbarcelona.org/MCDNA/). MC_DNA is a component of the Multiscale Genomics project where a unified view of the genome at all length scales from base-pair to chromosome in form of a webserver is developed.