Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA–Protein Complexes
Maxwell R. Tucker, Stefano Piana, Dazhi Tan, Michael V. Levine, David E. Shaw
Abstract
. Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, especially for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein-nucleic acid complexes.
Topics & Concepts
DNADouble strandedField (mathematics)Force field (fiction)MoleculeBiophysicsNanotechnologyChemical physicsPhysicsMaterials scienceChemistryBiologyBiochemistryQuantum mechanicsMathematicsPure mathematicsDNA and Nucleic Acid ChemistryRNA and protein synthesis mechanismsBacteriophages and microbial interactions