(Q34225993)

31 July 2017

Studying functional dynamics in bio-molecules using accelerated molecular dynamics (English)

1 reference

31 July 2017

2

J Andrew McCammon

1 reference

31 July 2017

Phineus R L Markwick

1

1 reference

PubMed ID

22015376

31 July 2017

language of work or name

English

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publication date

21 October 2011

1 reference

Physical Chemistry Chemical Physics

31 July 2017

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31 July 2017

13

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31 July 2017

45

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31 July 2017

20053-20065

1 reference

The Energy Landscapes and Motions of Proteins

31 July 2017

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

A perspective on enzyme catalysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Atomic-level characterization of the structural dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Taming the complexity of protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Multiscale modeling of biomolecular systems: in serial and in parallel

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Resolution exchange simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Discrete molecular dynamics simulations of peptide aggregation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Coarse-grained models for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

A natural coarse graining for simulating large biomolecular motion

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Loop motions of triosephosphate isomerase observed with elastic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Implicit solvent simulation models for biomembranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Multiscale simulation of transmembrane proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Long-timescale simulation methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Novel methods of sampling phase space in the simulation of biological systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

A dynamic model for the allosteric mechanism of GroEL

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

On the application of accelerated molecular dynamics to liquid water simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Accelerated entropy estimates with accelerated dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Application of the accelerated molecular dynamics simulations to the folding of a small protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Relating kinetic rates and local energetic roughness by accelerated molecular-dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Insight into the role of hydration on protein dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Prion and water: tight and dynamical hydration sites have a key role in structural stability

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Interfacial water structure controls protein conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Water mediation in protein folding and molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Structural biology by NMR: structure, dynamics, and interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Toward a unified representation of protein structural dynamics in solution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

21 January 2018

1 reference

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Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration

21 January 2018

1 reference

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

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Optimal estimates of free energies from multistate nonequilibrium work data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Statistically optimal analysis of samples from multiple equilibrium states

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

21 January 2018

1 reference

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On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

21 January 2018

1 reference

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Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Computing time scales from reaction coordinates by milestoning.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Implementation of Accelerated Molecular Dynamics in NAMD

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

Defining Long-Range Order and Local Disorder in Native α-Synuclein Using Residual Dipolar Couplings

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC1CP22100K

21 January 2018

Identifiers

DOI

10.1039/C1CP22100K

1 reference

31 July 2017

1 reference

PubMed ID

22015376