Ivani…Orozco {Nat Methods 13: 55}
Structural models of some of the molecular systems used to validate the Parmbsc1 force-field. The complete repertoire of structures includes more than 100 systems, with DNA and complexes of DNA with proteins and drugs among them.
Parmbsc1: a refined force field for DNA simulations
Ivani I, Dans PD, Noy A, Pérez A, Faustino I, Hospital A, Walther J, Andrio P, Goñi R, Balaceanu A, Portella G, Battistini F,, Gelpí JL, González C, Vendruscolo M, Laughton CA, Harris SA, Case DA, Orozco M.
Nat Methods 2016 Jan; 13: 55. [Epub 16 Nov. 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/.
PubMed: 26569599. Doi: 10.1038/nmeth.3658
