Implicit solvent models in molecular dynamics simulations: A brief overview
A Onufriev - Annual Reports in Computational Chemistry, 2008 - Elsevier
Implicit solvent framework is briefly introduced, with the focus on its advantages and
limitations for use in molecular simulations. The hierarchy of approximations that leads to …
limitations for use in molecular simulations. The hierarchy of approximations that leads to …
Helicase mechanisms and the coupling of helicases within macromolecular machines part I: structures and properties of isolated helicases
E Delagoutte, PH Von Hippel - Quarterly reviews of biophysics, 2002 - cambridge.org
1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take
advantage of 'breathing'fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs …
advantage of 'breathing'fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs …
Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure
MW Konrad, JI Bolonick - Journal of the American Chemical …, 1996 - ACS Publications
Molecular dynamics simulations were used to model the response of several double-
stranded dodecamers to gradually increasing tension applied to the opposing 3 'ends of the …
stranded dodecamers to gradually increasing tension applied to the opposing 3 'ends of the …
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
P Ferrara, J Apostolakis, A Caflisch - The Journal of Physical …, 2000 - ACS Publications
The folding of an α-helix and a β-hairpin was studied by 862 molecular dynamics
simulations with an implicit solvation model that allowed sampling of a total of 4 μs. The …
simulations with an implicit solvation model that allowed sampling of a total of 4 μs. The …
Local dielectric environment of B-DNA in solution: results from a 14 ns molecular dynamics trajectory
The dielectric behavior of solvent water around DNA is elicited in terms of Kirkwood−
Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a …
Grunwald theory from a 14 ns molecular dynamics trajectory of B-DNA developed in a …
B I - B II transitions in B-DNA
B Hartmann, D Piazzola, R Lavery - Nucleic acids research, 1993 - academic.oup.com
Molecular modelling is used to study the conformational and energetic aspects of B IB II
transitions within the backbone of a B-DNA dodecamer d (CATGACGTCATG) whose fine …
transitions within the backbone of a B-DNA dodecamer d (CATGACGTCATG) whose fine …
Detection of localized DNA flexibility
JD Kahn, E Yun, DM Crothers - Nature, 1994 - nature.com
THE bending and flexibility of DNA are important in packaging, recombination and
transcription1–3. Bending decreases electrophoretic mobility in a manner depending on …
transcription1–3. Bending decreases electrophoretic mobility in a manner depending on …
Involvement of Fis protein in replication of the Escherichia coli chromosome
M Filutowicz, W Ross, J Wild, RL Gourse - Journal of bacteriology, 1992 - Am Soc Microbiol
We report evidence indicating that Fis protein plays a role in initiation of replication at oriC in
vivo. At high temperatures, fis null mutants form filamentous cells, show aberrant nucleoid …
vivo. At high temperatures, fis null mutants form filamentous cells, show aberrant nucleoid …
Targeted Base Stacking Disruption by the EcoRI DNA Methyltransferase
BW Allan, NO Reich - Biochemistry, 1996 - ACS Publications
We describe a novel fluorescence-based assay for detecting DNA conformational alterations
within enzyme− DNA complexes. The target adenine for Eco RI DNA methyltransferase …
within enzyme− DNA complexes. The target adenine for Eco RI DNA methyltransferase …
Kinetics and energetics of base-pair opening in 5'-d (CGCGAATTCGCG)-3'and a substituted dodecamer containing G. cntdot. T mismatches
JG Moe, IM Russu - Biochemistry, 1992 - ACS Publications
Revised Manuscript Received June 9, 1992 abstract: Proton nuclear magnetic resonance
(NMR) spectroscopy is used to characterize the kinetics and energetics of base-pair opening …
(NMR) spectroscopy is used to characterize the kinetics and energetics of base-pair opening …