Implicit solvent simulations of DNA and DNA-protein complexes: Agreement with explicit solvent vs. experiment
Article Abstract:
Stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. The results have suggested that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations and furthermore, partial conformational transitions toward A-DNA conformations are observed when salt is added within the implicit solvent framework.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model
Article Abstract:
The heterogenous dielectric generalized Born (HDGB) methodology is an extension of the GBMV model for the simulation of integral membrane proteins with an implicit membrane environment. Three large integral membrane proteins were simulated with the HDGB model in order to evaluate how well thermodynamic and dynamic properties are reproduced.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations
Article Abstract:
The sampling of pi-helical conformations is investigated using empirical force fields. Observation of pi-helical conformations in molecular dynamics is a force field artifact.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2003
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