(Q40406047)

20 September 2017

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms (English)

1 reference

20 September 2017

6

Gunnar Carlsson

1 reference

20 September 2017

Xuhui Huang

1

1 reference

20 September 2017

Yuan Yao

2

1 reference

20 September 2017

Gregory R Bowman

3

1 reference

20 September 2017

Jian Sun

4

1 reference

20 September 2017

Leonidas J Guibas

5

1 reference

20 September 2017

Vijay S Pande

7

1 reference

20 September 2017

1 January 2010

1 reference

Pacific Symposium on Biocomputing

20 September 2017

1 reference

20 September 2017

228-239

1 reference

Rapid equilibrium sampling initiated from nonequilibrium data

20 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Using generalized ensemble simulations and Markov state models to identify conformational states

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Rearrangement of partially ordered stacked conformations contributes to the rugged energy landscape of a small RNA hairpin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Translation at the single-molecule level

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Transition networks for modeling the kinetics of conformational change in macromolecules

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

COMPUTING: Screen Savers of the World Unite!

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

The molecular basis of eukaryotic transcription

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

DNA folding and melting observed in real time redefine the energy landscape

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Argonaute and RNA--getting into the groove

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Coarse-grained models for proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Does water play a structural role in the folding of small nucleic acids?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Self-assembly of peptides into a beta-barrel motif

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Orientational potentials extracted from protein structures improve native fold recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Protein folding and misfolding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Coarse-grained sequences for protein folding and design

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Canonical dynamics: Equilibrium phase-space distributions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Hierarchy and dynamics of RNA folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Computer simulation of protein folding

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Topological methods for exploring low-density states in biomolecular folding pathways

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Structural insight into RNA hairpin folding intermediates

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Tetraloops and RNA folding

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Coarse master equations for peptide folding dynamics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Computing time scales from reaction coordinates by milestoning.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4423759

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19908375

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Exploring the energy landscape of a small RNA hairpin

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19908375

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19908375

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

1 reference

20 September 2017

PubMed publication ID

19908375

1 reference