MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale (Q39373045)

11 September 2017

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale (English)

1 reference

11 September 2017

6

Vijay S Pande

1 reference

11 September 2017

1

Kyle A Beauchamp

1 reference

11 September 2017

Gregory R Bowman

2

1 reference

11 September 2017

Thomas J Lane

series ordinal

3

1 reference

11 September 2017

Lutz Maibaum

series ordinal

4

1 reference

11 September 2017

Imran S Haque

series ordinal

5

1 reference

11 September 2017

1 October 2011

1 reference

Journal of Chemical Theory and Computation

11 September 2017

1 reference

11 September 2017

7

1 reference

11 September 2017

10

1 reference

11 September 2017

3412-3419

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Enhanced modeling via network theory: Adaptive sampling of Markov state models

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Equilibrium distribution from distributed computing (simulations of protein folding).

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Making connections between ultrafast protein folding kinetics and molecular dynamics simulations

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Atomic-level characterization of the structural dynamics of proteins

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Improved side-chain torsion potentials for the Amber ff99SB protein force field

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Comparing geometric and kinetic cluster algorithms for molecular simulation data

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Building Markov state models along pathways to determine free energies and rates of transitions

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Transition networks for modeling the kinetics of conformational change in macromolecules

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Protein folding studied by single-molecule FRET.

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Structure-function-folding relationship in a WW domain

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Sub-microsecond protein folding

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Gaussian-weighted RMSD superposition of proteins: a structural comparison for flexible proteins and predicted protein structures

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Myosin IXb is a single-headed minus-end-directed processive motor

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Principles that govern the folding of protein chains

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Protein structure determination in solution by NMR spectroscopy

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Progress and challenges in the automated construction of Markov state models for full protein systems

11 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Protein folding intermediates: native-state hydrogen exchange

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Markov state models based on milestoning.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Markov models of molecular kinetics: generation and validation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Coarse master equations for peptide folding dynamics.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3224091

Sequence-specific dynamics modulate recognition specificity in WW domains

21 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22125474

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT200463M

1 reference

11 September 2017

1 reference

11 September 2017

1 reference