(Q37145710)

18 August 2017

A novel implicit solvent model for simulating the molecular dynamics of RNA (English)

1 reference

18 August 2017

3

Tobin R Sosnick

1 reference

18 August 2017

4

Karl F Freed

1 reference

18 August 2017

Yufeng Liu

1

1 reference

18 August 2017

Esmael Haddadian

series ordinal

2

1 reference

18 August 2017

Haipeng Gong

series ordinal

5

1 reference

18 August 2017

language of work or name

English

0 references

publication date

1 September 2013

1 reference

18 August 2017

1 reference

18 August 2017

105

1 reference

18 August 2017

5

1 reference

18 August 2017

1248-1257

1 reference

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Evaluation of DNA Force Fields in Implicit Solvation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Extended structures in RNA folding intermediates are due to nonnative interactions rather than electrostatic repulsion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Long-timescale molecular dynamics simulations of protein structure and function.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of membrane channels and transporters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

A short guide for molecular dynamics simulations of RNA systems.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born model.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of nucleic acid-protein complexes.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of RNA: an in silico single molecule approach.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Folding very short peptides using molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of sarcin-ricin rRNA motif.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Effects of base substitutions in an RNA hairpin from molecular dynamics and free energy simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Effective Born radii in the generalized Born approximation: the importance of being perfect

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Control of the selectivity of the aquaporin water channel family by global orientational tuning

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Electrostatics of nanosystems: application to microtubules and the ribosome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Crystal structure of the ribosomal RNA domain essential for binding elongation factors

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Treecode-based generalized Born method.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Langevin-Debye model for nonlinear electrostatic screening of solvated ions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Dielectric saturation of the ion hydration shell and interaction between two double helices of DNA in mono- and multivalent electrolyte solutions: foundations of the epsilon-modified Poisson-Boltzmann theory.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Ion solvation thermodynamics from simulation with a polarizable force field

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

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

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute−Water Clusters

20 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3762369

Extension of the MST continuum solvation model to the RM1 semiempirical hamiltonian

4 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24010668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24010668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

All-atom fast protein folding simulations: the villin headpiece

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24010668

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2013.07.033

1 reference

18 August 2017

1 reference

18 August 2017

PubMed publication ID

24010668

1 reference