Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model (Q40144576)

17 September 2017

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model (English)

1 reference

17 September 2017

Williams DJ

1

1 reference

PMCID

1300288

17 September 2017

Hall KB

series ordinal

2

1 reference

PMCID

1300288

17 September 2017

language of work or name

English

0 references

publication date

1 June 1999

1 reference

17 September 2017

1 reference

17 September 2017

76

1 reference

17 September 2017

6

1 reference

17 September 2017

3192-3205

1 reference

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

17 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Hydration of the RNA duplex r(CGCAAAUUUGCG)2 determined by NMR.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Understanding the thermodynamic stability of an RNA hairpin and its mutant

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Structure of the P1 helix from group I self-splicing introns

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Energetic coupling between DNA bending and base pair opening

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Treatment of electrostatic effects in macromolecular modeling

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

What affects the effect of 2'-alkoxy modifications? 1. Stabilization effect of 2'-methoxy substitutions in uniformly modified DNA oligonucleotides

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Structure of an unusually stable RNA hairpin

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

A potential smoothing algorithm accurately predicts transmembrane helix packing.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Molecular dynamics analysis of a ribonuclease C-peptide analogue

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300288

Rules governing the orientation of the 2'-hydroxyl group in RNA

20 August 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Accurate modeling of the intramolecular electrostatic energy of proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Solvent effects on the dynamics of (dG-dC)3

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Distance-dependent dielectric constants and their application to double-helical DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

Semianalytical treatment of solvation for molecular mechanics and dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

A Leap-frog Algorithm for Stochastic Dynamics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977471-0

10.1016/S0006-3495(99)77471-0

7 January 2021

Identifiers

DOI

1 reference

17 September 2017

1 reference

17 September 2017

1 reference

PMCID

1300288