explicit solvent molecular dynamics simulations (Molecular Dynamics Inc)
90
Structured Review
Molecular Dynamics Inc
explicit solvent molecular dynamics simulations
Explicit Solvent Molecular Dynamics Simulations, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/explicit+solvent+molecular+dynamics+simulations/explicit+solvent+molecular+dynamics/pmc11381966__CC___060___D4CC02125H___s001-37-2-5
Average 90 stars, based on 1 article reviews
Explicit Solvent Molecular Dynamics Simulations, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/explicit+solvent+molecular+dynamics+simulations/explicit+solvent+molecular+dynamics/pmc11381966__CC___060___D4CC02125H___s001-37-2-5
Average 90 stars, based on 1 article reviews
explicit solvent molecular dynamics simulations - by Bioz Stars,
2026-10
90/100 stars
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other:Article Title: Using small angle scattering (SAS) to structurally characterise peptide and protein self-assembled materials. Article Snippet: This article was published as part of the Peptide- and protein-based materials themed issue Guest editors Rein Ulijn and Dek Woolfson Please take a look at the issue 9 2010 table of contents to access other reviews in this themed issue Pu bl is he d on 2 6 N ov em be r 20 10 .. D ow nl oa de d by W A SH B U R N U N IV E R SI T Y o n 22 /1 0/ 20 14 1 6: 05 :3 0.. View Article Online / Journal Homepage / Table of Contents for this issue 1200 Chem. Solvent:Article Title: Atomic Radii for Continuum Electrostatics Calculations on Nucleic Acids Article Snippet: The accuracy of continuum electrostatic models, in which the solvent is represent as a featureless dielectric medium, depends sensitively on the choice of the atomic radii used for setting the dielectric boundary between the solute and the solvent.. Here, a set of optimal atomic radii for performing accurate continuum electrostatic calculations on naturally occurring nucleic acids is parametrized using molecular dynamics simulations and free energy perturbation calculations with explicit water molecules.. Small model compounds constituting the building blocks of nucleic acids (base, sugar, phosphate) as well as combinations of these units (nucleoside, diphosphate sugar) are chosen to get proper representation of all the molecular moieties found in nucleic acids. Article Title: QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. Article Snippet: A set of conformations obtained from explicit solvent molecular dynamics (MD) simulations of the Sarcin−Ricin internal loop (SRL) RNA motif is investigated using quantum mechanical (QM, TPSS-D3/def2-TZVP DFT-D3) and molecular mechanics (MM, AMBER parm99bsc0+χol3 force field) methods.. Solvent effects are approximated using implicit solvent methods (COSMO for DFT-D3; GB and PB for MM).. Large-scale DFT-D3 optimizations of the full 11nucleotide motif are compared to MM results and reveal a higher flexibility of DFT-D3 over the MM in the optimization procedure. Article Title: Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. Article Snippet: Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached.. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date.. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Modification:Article Title: Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. Article Snippet: Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached.. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date.. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Derivative Assay:Article Title: Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. Article Snippet: Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached.. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date.. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Comparison:Article Title: Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. Article Snippet: Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached.. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date.. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. |