Development and current status of the CHARMM force field for nucleic acids
AD MacKerell Jr, N Banavali… - … : original Research on …, 2000 - Wiley Online Library
The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model
for investigations of nucleic acids via empirical force field calculations. The force field …
for investigations of nucleic acids via empirical force field calculations. The force field …
Molecular dynamics simulation of nucleic acids: successes, limitations, and promise
TE Cheatham III, MA Young - Biopolymers: Original Research …, 2000 - Wiley Online Library
In the last five years we have witnessed a significant increase in the number publications
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …
describing accurate and reliable all‐atom molecular dynamics simulations of nucleic acids …
All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
N Foloppe, AD MacKerell, Jr - Journal of computational …, 2000 - Wiley Online Library
Empirical force‐field calculations on biological molecules represent an effective method to
obtain atomic detail information on the relationship of their structure to their function. Results …
obtain atomic detail information on the relationship of their structure to their function. Results …
All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
AD MacKerell Jr, NK Banavali - Journal of computational …, 2000 - Wiley Online Library
Molecular dynamics simulations based on empirical force fields can greatly enhance
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …
knowledge of DNA and RNA structure and dynamics in solution. Presented are results on …
An improved empirical potential energy function for molecular simulations of phospholipids
SE Feller, AD MacKerell - The Journal of Physical Chemistry B, 2000 - ACS Publications
Improvements in the CHARMM all-atom force field for atomic-level molecular simulations of
lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) …
lipids are reported. Substantial adjustments have been made to the Lennard-Jones (LJ) …
Molecular dynamics simulation of nucleic acids
TE Cheatham III, PA Kollman - Annual review of physical …, 2000 - annualreviews.org
We review molecular dynamics simulations of nucleic acids, including those completed from
1995 to 2000, with a focus on the applications and results rather than the methods. After the …
1995 to 2000, with a focus on the applications and results rather than the methods. After the …
[HTML][HTML] On the truncation of long-range electrostatic interactions in DNA
J Norberg, L Nilsson - Biophysical journal, 2000 - cell.com
Long-range interactions are known to play an important role in highly polar biomolecules
like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate …
like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate …
Modeling DNA deformations
WK Olson, VB Zhurkin - Current opinion in structural biology, 2000 - Elsevier
Recent developments have been made in modeling double-helical DNA at four levels of
three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is …
three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is …
Nucleic acids: theory and computer simulation, Y2K
DL Beveridge, KJ McConnell - Current opinion in structural biology, 2000 - Elsevier
Molecular dynamics simulations on DNA and RNA that include solvent are now being
performed under realistic environmental conditions of water activity and salt. Improvements …
performed under realistic environmental conditions of water activity and salt. Improvements …
Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations
J Šponer, I Berger, N Špačková… - Journal of …, 2000 - Taylor & Francis
Aromatic stacking of nucleic acid bases is one of the key players in determining the structure
and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive …
and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive …