Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr - Journal of computational chemistry, 2004 - Wiley Online Library
Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
Simulation and modeling of nucleic acid structure, dynamics and interactions
TE Cheatham III - Current opinion in structural biology, 2004 - Elsevier
In moving towards the simulation of larger nucleic acid assemblies over longer timescales
that include more accurate representations of the environment, we are nearing the end of an …
that include more accurate representations of the environment, we are nearing the end of an …
Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational …
AD Mackerell Jr, M Feig… - Journal of computational …, 2004 - Wiley Online Library
Computational studies of proteins based on empirical force fields represent a powerful tool
to obtain structure–function relationships at an atomic level, and are central in current efforts …
to obtain structure–function relationships at an atomic level, and are central in current efforts …
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d (CpG) steps
We describe herein a computationally intensive project aimed at carrying out molecular
dynamics (MD) simulations including water and counterions on B-DNA oligomers containing …
dynamics (MD) simulations including water and counterions on B-DNA oligomers containing …
Structure and axis curvature in two dA6·dT6 DNA oligonucleotides: Comparison of molecular dynamics simulations with results from crystallography and NMR …
SB Dixit, F Pitici, DL Beveridge - … : Original Research on …, 2004 - Wiley Online Library
Molecular dynamics (MD) simulations have been performed on the A6 containing DNA
dodecamers d (GGCAAAAAACGG) solved by NMR and d (CGCAAAAAAGCG) solved by …
dodecamers d (GGCAAAAAACGG) solved by NMR and d (CGCAAAAAAGCG) solved by …
A combined quantum mechanics and molecular dynamics study of charge transfer in DNA
K Siriwong - 2004 - mediatum.ub.tum.de
We employ a combined quantum mechanics (QM) and molecular dynamics (MD) approach
for the computational study of charge transfer in DNA. Three key parameters that control the …
for the computational study of charge transfer in DNA. Three key parameters that control the …
[PDF][PDF] Surjit B. Dixit Felicia Pitici
DL Beveridge - Biopolymers, 2004 - academia.edu
Molecular dynamics (MD) simulations have been performed on the A6 containing DNA
dodecamers d (GGCAAAAAACGG) solved by NMR and d (CGCAAAAAAGCG) solved by …
dodecamers d (GGCAAAAAACGG) solved by NMR and d (CGCAAAAAAGCG) solved by …