Perspective: Markov models for long-timescale biomolecular dynamics (Q41774653)

9 October 2017

Perspective: Markov models for long-timescale biomolecular dynamics (English)

1 reference

9 October 2017

C R Schwantes

1

1 reference

9 October 2017

R T McGibbon

series ordinal

2

1 reference

9 October 2017

V S Pande

series ordinal

3

1 reference

9 October 2017

language of work or name

English

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publication date

1 September 2014

1 reference

Journal of Chemical Physics

9 October 2017

1 reference

9 October 2017

141

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9 October 2017

9

1 reference

9 October 2017

090901

1 reference

EMMA: A Software Package for Markov Model Building and Analysis.

9 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Complex pathways in folding of protein G explored by simulation and experiment.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

A molecular interpretation of 2D IR protein folding experiments with Markov state models

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Activation pathway of Src kinase reveals intermediate states as targets for drug design

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Quantitative comparison of alternative methods for coarse-graining biological networks

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Recovery from slow inactivation in K+ channels is controlled by water molecules

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Systematic improvement of a classical molecular model of water

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

To milliseconds and beyond: challenges in the simulation of protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Kinetic characterization of the critical step in HIV-1 protease maturation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Evaluation and optimization of discrete state models of protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Characterization and rapid sampling of protein folding Markov state model topologies

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

How fast-folding proteins fold

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Structure-based drug design to augment hit discovery

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

How robust are protein folding simulations with respect to force field parameterization?

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Challenges in protein folding simulations: Timescale, representation, and analysis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Atomistic folding simulations of the five-helix bundle protein λ(6−85).

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Everything you wanted to know about Markov State Models but were afraid to ask

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

High-throughput all-atom molecular dynamics simulations using distributed computing.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Elucidating the inhibition mechanism of HIV-1 non-nucleoside reverse transcriptase inhibitors through multicopy molecular dynamics simulations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Accelerating molecular dynamic simulation on graphics processing units

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

COMPUTING: Screen Savers of the World Unite!

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Protein folding pathways from replica exchange simulations and a kinetic network model

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Gene prediction with a hidden Markov model and a new intron submodel

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

The use of constitutively active GPCRs in drug discovery and functional genomics

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Molecular dynamics simulations of biomolecules

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Oligomerization of opioid receptors with beta 2-adrenergic receptors: a role in trafficking and mitogen-activated protein kinase activation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

The beta2-adrenergic receptor/betaarrestin complex recruits the clathrin adaptor AP-2 during endocytosis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Reaction path study of conformational transitions and helix formation in a tetrapeptide

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Variational Approach to Molecular Kinetics.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Statistical model selection for Markov models of biomolecular dynamics

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Identification of slow molecular order parameters for Markov model construction

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Markov models of molecular kinetics: generation and validation

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Coarse master equations for peptide folding dynamics.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Computing time scales from reaction coordinates by milestoning.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Folding of the GB1 hairpin peptide from discrete path sampling.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4156582

Anton, a special-purpose machine for molecular dynamics simulation

18 August 2018

1 reference

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

21 January 2018

1 reference

A tutorial on hidden Markov models and selected applications in speech recognition

21 January 2018

1 reference

CONSTRUCTING MULTI-RESOLUTION MARKOV STATE MODELS (MSMS) TO ELUCIDATE RNA HAIRPIN FOLDING MECHANISMS

21 January 2018

1 reference

A simple polarizable model of water based on classical Drude oscillators

21 January 2018

1 reference

Small-world networks and the conformation space of a short lattice polymer chain

21 January 2018

1 reference

Energy landscape of a small peptide revealed by dihedral angle principal component analysis

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25194354

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25194354

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The protein folding network

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25194354

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4895044

1 reference

9 October 2017

1 reference

0 references

1 reference

9 October 2017

PubMed publication ID

25194354

1 reference