(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

17 September 2017

Hall KB

series ordinal

2

1 reference

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

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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

PubMed publication ID

10354444

1 reference