(Q81131493)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18428877%20AND%20SRC:MED&resulttype=core&format=json

6 January 2020

title

Molecular modeling of nucleic acid structure: electrostatics and solvation (English)

1 reference

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6 January 2020

author name string

T E Cheatham

series ordinal

1

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6 January 2020

B R Brooks

series ordinal

2

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6 January 2020

P A Kollman

series ordinal

3

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6 January 2020

publication date

1 August 2001

1 reference

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Current protocols in nucleic acid chemistry / editorial board, Serge L. Beaucage ... [et al.]

6 January 2020

published in

1 reference

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6 January 2020

volume

Chapter 7

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6 January 2020

page(s)

Unit 7.9

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The ABCs of molecular dynamics simulations on B-DNA, circa 2012.

6 January 2020

cites work

1 reference

12 December 2020

Molecular dynamics simulation of nucleic acids

1 reference

12 December 2020

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

1 reference

12 December 2020

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

1 reference

12 December 2020

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor

1 reference

12 December 2020

Theory and applications of the generalized Born solvation model in macromolecular simulations

1 reference

12 December 2020

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.

1 reference

12 December 2020

An accurate and simple quantum model for liquid water

1 reference

12 December 2020

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

1 reference

12 December 2020

An efficient hybrid explicit/implicit solvent method for biomolecular simulations

1 reference

12 December 2020

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

1 reference

12 December 2020

Electrostatics of nanosystems: application to microtubules and the ribosome

1 reference

12 December 2020

Molecular dynamics simulations and their application to four-stranded DNA.

1 reference

12 December 2020

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

1 reference

12 December 2020

Computer simulation of DNA double-helix dynamics

1 reference

12 December 2020

The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations.

1 reference

12 December 2020

Origin of DNA helical structure and its sequence dependence

1 reference

12 December 2020

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

1 reference

12 December 2020

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1 reference

12 December 2020

CHARMM: the biomolecular simulation program

1 reference

12 December 2020

Calculations of electrostatic interactions in biological systems and in solutions

1 reference

12 December 2020

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

1 reference

12 December 2020

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

12 December 2020

Molecular mechanics calculations of dA12.dT12 and of the curved molecule d(GCTCGAAAAA)4.d(TTTTTCGAGC)4

1 reference

12 December 2020

A computational study of nucleosomal DNA flexibility

1 reference

12 December 2020

Structure of a B-DNA dodecamer. III. Geometry of hydration

1 reference

12 December 2020

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

1 reference

12 December 2020

The inclusion of electrostatic hydration energies in molecular mechanics calculations

1 reference

12 December 2020

Generalized born models of macromolecular solvation effects

1 reference

12 December 2020

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

12 December 2020

A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

1 reference

12 December 2020

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

1 reference

12 December 2020

Evaluating rotational diffusion from protein MD simulations

1 reference

12 December 2020

A molecular dynamics simulation of double-helical B-DNA including counterions and water

1 reference

12 December 2020

The electrostatic contribution to the B to Z transition of DNA.

1 reference

12 December 2020

Coupling of local folding to site-specific binding of proteins to DNA

1 reference

12 December 2020

A free energy analysis of nucleic acid base stacking in aqueous solution

1 reference

12 December 2020

A mesoscale model of DNA and its renaturation

1 reference

12 December 2020

Canonical dynamics: Equilibrium phase-space distributions

1 reference

12 December 2020

Multiple grid methods for classical molecular dynamics.

1 reference

12 December 2020

A quantum mechanical polarizable force field for biomolecular interactions

1 reference

12 December 2020

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

1 reference

12 December 2020

Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides

1 reference

12 December 2020

Coarse-grained simulations of macromolecules: from DNA to nanocomposites

1 reference

12 December 2020

On the truncation of long-range electrostatic interactions in DNA.

1 reference

12 December 2020

Biomolecular electrostatics and solvation: a computational perspective

1 reference

12 December 2020

Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations

1 reference

12 December 2020

Minor groove-binding architectural proteins: structure, function, and DNA recognition.

1 reference

12 December 2020

The electrostatic contribution to DNA base-stacking interactions.

1 reference

12 December 2020

Evaluation of DNA Force Fields in Implicit Solvation

1 reference

12 December 2020

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

1 reference

12 December 2020

Molecular dynamics simulations of d(C-G-C-G-A) X d(T-C-G-C-G) with and without "hydrated" counterions

1 reference

12 December 2020

Electrostatic interactions in macromolecules: theory and applications

1 reference

12 December 2020

Inhibitor-induced structural change in the HCV IRES domain IIa RNA

1 reference

12 December 2020

Fast algorithms for classical physics.

1 reference

12 December 2020

Computational exploration of mobile ion distributions around RNA duplex

1 reference

12 December 2020

Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water.

1 reference

12 December 2020

Dominant forces in protein folding

1 reference

12 December 2020

pH-dependent dynamics of complex RNA macromolecules

1 reference

12 December 2020

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

1 reference

12 December 2020

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

1 reference

12 December 2020

Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements

1 reference

12 December 2020

Electrostatics calculations: latest methodological advances

1 reference

12 December 2020

Generalized Born model with a simple, robust molecular volume correction

1 reference

12 December 2020

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment

1 reference

12 December 2020

Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations

1 reference

12 December 2020

Local DNA stretching mimics the distortion caused by the TATA box-binding protein

1 reference

12 December 2020

Salt effects on ligand-DNA binding. Minor groove binding antibiotics.

1 reference

12 December 2020

A modified TIP3P water potential for simulation with Ewald summation

1 reference

12 December 2020

RNA stability under different combinations of amber force fields and solvation models

1 reference

12 December 2020

Solvation energy in protein folding and binding

1 reference

12 December 2020

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

1 reference

12 December 2020

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

12 December 2020

Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method

1 reference

12 December 2020

Energetic coupling between DNA bending and base pair opening

1 reference

12 December 2020

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

1 reference

12 December 2020

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

1 reference

12 December 2020

The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

1 reference

12 December 2020

Molecular dynamics simulations of nucleic acid-protein complexes.

1 reference

12 December 2020

Modeling DNA in aqueous solutions: theoretical and computer simulation studies on the ion atmosphere of DNA.

1 reference

12 December 2020

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

1 reference

12 December 2020

DNA and its counterions: a molecular dynamics study

1 reference

12 December 2020

Frontiers in molecular dynamics simulations of DNA.

1 reference

12 December 2020

Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure

1 reference

12 December 2020

Static and statistical bending of DNA evaluated by Monte Carlo simulations

1 reference

12 December 2020

Treatment of electrostatic effects in macromolecular modeling

1 reference

12 December 2020

Glass transition in DNA from molecular dynamics simulations

1 reference

12 December 2020

Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. The reaction field method.

1 reference

12 December 2020

Modelling extreme stretching of DNA.

1 reference

12 December 2020

Solvent-accessible surfaces of nucleic acids

1 reference

12 December 2020

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

1 reference

12 December 2020

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids

1 reference

12 December 2020

Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing

1 reference

12 December 2020

Solvent effects on model d(CG.G)7 and d(TA.T)7 DNA triple helices

1 reference

12 December 2020

Exploring protein native states and large-scale conformational changes with a modified generalized born model

1 reference

12 December 2020

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

1 reference

12 December 2020

Theory of electrostatic interactions in macromolecules

1 reference

12 December 2020

Isotropic periodic sum: a method for the calculation of long-range interactions.

1 reference

12 December 2020

Molecular dynamics simulations of small peptides: dependence on dielectric model and pH.

1 reference

12 December 2020

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

1 reference

12 December 2020

Electrostatic Energy and Macromolecular Function

1 reference

12 December 2020

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

1 reference

12 December 2020

A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions

1 reference

12 December 2020

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

1 reference

12 December 2020

Cations in charge: magnesium ions in RNA folding and catalysis

1 reference

12 December 2020

10.1002/0471142700.NC0709S05

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18428877%20AND%20SRC:MED&resulttype=core&format=json

6 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18428877%20AND%20SRC:MED&resulttype=core&format=json

6 January 2020

PubMed publication ID

18428877

1 reference