Parmbsc1: a refined force field for DNA simulations.

Ivan IvaniPablo Daniel DansAgnes NoyAlberto PérezIgnacio FaustinoAdam HospitalJürgen WaltherPau AndrioRamon GoñiAlexandra BalaceanuGuillem PortellaFederica BattistiniJosep Lluis Gelpí Carlos GonzálezMichele VendruscoloCharles A LaughtonSarah A HarrisDavid A CaseModesto Orozco

Published in: Nature methods (2015)

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.

Keyphrases

single molecule
circulating tumor
cell free
molecular dynamics
depressive symptoms
nucleic acid
electronic health record
big data
circulating tumor cells
machine learning
molecular dynamics simulations
monte carlo
virtual reality
deep learning
data analysis