Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
M Zgarbová, M Otyepka, J Sponer… - Journal of chemical …, 2011 - ACS Publications
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …
field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 …
Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model
CM Baker, VM Anisimov… - The journal of physical …, 2011 - ACS Publications
A polarizable force field for nucleic acid bases based on the classical Drude oscillator model
is presented. Parameter optimization was performed to reproduce crystallographic …
is presented. Parameter optimization was performed to reproduce crystallographic …
Evaluation of DNA force fields in implicit solvation
T Gaillard, DA Case - Journal of chemical theory and computation, 2011 - ACS Publications
DNA structural deformations and dynamics are crucial to its interactions in the cell.
Theoretical simulations are essential tools used to explore the structure, dynamics, and …
Theoretical simulations are essential tools used to explore the structure, dynamics, and …
[HTML][HTML] Communication: Quantum polarized fluctuating charge model: A practical method to include ligand polarizability in biomolecular simulations
S Roy Kimura, R Rajamani, DR Langley - The Journal of chemical …, 2011 - pubs.aip.org
We present a simple and practical method to include ligand electronic polarization in
molecular dynamics (MD) simulation of biomolecular systems. The method involves …
molecular dynamics (MD) simulation of biomolecular systems. The method involves …
A theoretical investigation examining DNA conformational changes and their effects on glycosylase function
AR Brice - 2011 - search.proquest.com
Glycosylase enzymes initiate the process of base excision repair (BER) in order to prevent
the irreversible modification of the genome. In the BER process a damaged DNA base is …
the irreversible modification of the genome. In the BER process a damaged DNA base is …