Atomic-Level Force-Field Simulation of DNA Movement: Its Folding into Double, Triple, Quadruple Strands & Interactions with Proteins & Drugs at Timescales of Picoseconds to Minutes & System Sizes from Nanometers to Meter

A simulation method developed in Spain allows the study—with unprecedented accuracy—of structural changes in DNA and of the interaction of DNA with proteins and drugs. Molecular dynamics is a technique that allows the simulation of DNA movement, its folding into double, triple, or quadruple strands, and even its interaction with proteins and drugs. Molecular dynamics is used to address the processes that occur over time scales ranging from picoseconds to minutes and it can be used for molecular systems of various sizes, from few nanometers to a meter. Headed by Modesto Orozco, Ph.D., the Molecular Modelling and Bioinformatics Lab at the Institute for Research in Biomedicine (IRB Barcelona) is developing several theoretical methods to better understand the behavior of bio-macromolecules, in particular nucleic acids, on a wide spatial-temporal scale and with a focus on biomedical and biotech applications. The group has just published a new model in Nature Methods in an online article dated November 16, 2015. Developed in collaboration with the Barcelona SuperComputing Center (BSC) and laboratories in England and the US, this model allows atomic-level simulations of DNA dynamics and, to the great satisfaction of the researchers,“with extraordinary accuracy”—an achievement that has taken five years of work and the testing of more than 100 DNA systems. The Nature Methods article is titled “Parmbsc1: A Refined Force-Field for DNA Simulations.” The data are stored in a public website that currently holds more than 4 Terabytes of information: This web site is accessible through the Spanish Institute of Bioinformatics (INB) and the ELIXIR-Excellerate network, the largest collection of life sciences data in Europe, to which IRB Barcelona contributes.
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