Challenges in protein folding simulations: Timescale, representation, and analysis (Q34545688)

2 August 2017

title

Challenges in protein folding simulations: Timescale, representation, and analysis (English)

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2 August 2017

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Klaus Schulten

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2 August 2017

Peter L Freddolino

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2 August 2017

Christopher B Harrison

series ordinal

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2 August 2017

Yanxin Liu

series ordinal

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2 August 2017

publication date

1 October 2010

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2 August 2017

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2 August 2017

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2 August 2017

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2 August 2017

page(s)

751-758

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Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

2 August 2017

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Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions

7 July 2018

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Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding

7 July 2018

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Comparing geometric and kinetic cluster algorithms for molecular simulation data

7 July 2018

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A Survey of λ Repressor Fragments from Two-State to Downhill Folding

7 July 2018

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Current status of the AMOEBA polarizable force field

7 July 2018

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Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance

7 July 2018

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Common structural transitions in explicit-solvent simulations of villin headpiece folding

7 July 2018

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Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

7 July 2018

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Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis.

7 July 2018

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Force field bias in protein folding simulations

7 July 2018

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The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations

7 July 2018

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7 July 2018

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Computations of standard binding free energies with molecular dynamics simulations

7 July 2018

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The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier

7 July 2018

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Computing the stability diagram of the Trp-cage miniprotein

7 July 2018

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Diffusive reaction dynamics on invariant free energy profiles

7 July 2018

1 reference

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One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

7 July 2018

1 reference

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Are current molecular dynamics force fields too helical?

7 July 2018

1 reference

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Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

7 July 2018

1 reference

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Universality and diversity of folding mechanics for three-helix bundle proteins

7 July 2018

1 reference

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

7 July 2018

1 reference

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Accelerating molecular modeling applications with graphics processors

7 July 2018

1 reference

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Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

7 July 2018

1 reference

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Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy

7 July 2018

1 reference

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Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.

7 July 2018

1 reference

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Two-stage folding of HP-35 from ab initio simulations

7 July 2018

1 reference

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

7 July 2018

1 reference

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Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

7 July 2018

1 reference

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Understanding ensemble protein folding at atomic detail

7 July 2018

1 reference

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Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

7 July 2018

1 reference

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

7 July 2018

1 reference

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Structure-function-folding relationship in a WW domain

7 July 2018

1 reference

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Molecular dynamics: survey of methods for simulating the activity of proteins

7 July 2018

1 reference

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Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

7 July 2018

1 reference

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Testing simplified proteins models of the hPin1 WW domain

7 July 2018

1 reference

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Sub-microsecond protein folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Reaction coordinates and rates from transition paths

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Determination of ultrafast protein folding rates from loop formation dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

7 July 2018

1 reference

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Theory of protein folding

7 July 2018

1 reference

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CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations.

7 July 2018

1 reference

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Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

7 July 2018

1 reference

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Free energy landscape of protein folding in water: Explicit vs. implicit solvent

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

7 July 2018

1 reference

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Experimental tests of villin subdomain folding simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations

7 July 2018

1 reference

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Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

An improved hydrogen bond potential: impact on medium resolution protein structures.

7 July 2018

1 reference

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Designing a 20-residue protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Knowledge-based protein secondary structure assignment

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032381

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

7 July 2018

1 reference

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Studies in Molecular Dynamics. I. General Method

7 July 2018

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Interpeptide interactions induce helix to strand structural transition in Abeta peptides

21 January 2018

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Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution

21 January 2018

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Rate constant and reaction coordinate of Trp-cage folding in explicit water

21 January 2018

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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale.

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

21 January 2018

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

21 January 2018

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One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

21 January 2018

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Identification of the protein folding transition state from molecular dynamics trajectories.

21 January 2018

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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

21 January 2018

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Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

21 January 2018

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Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

21 January 2018

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An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

21 January 2018

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Electron density redistribution accounts for half the cooperativity of alpha helix formation.

21 January 2018

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Charge-on-spring polarizable water models revisited: From water clusters to liquid water to ice

21 January 2018

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Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

21 January 2018

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Comparison of simple potential functions for simulating liquid water

21 January 2018

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A polarizable model of water for molecular dynamics simulations of biomolecules

21 January 2018

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Critical assessment of methods of protein structure prediction - Round VIII.

21 January 2018

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Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator

27 October 2018

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Dynamic NMR Line-Shape Analysis Demonstrates that the Villin Headpiece Subdomain Folds on the Microsecond Time Scale

21 January 2018

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12 December 2020

A thermostable 35-residue subdomain within villin headpiece

1 reference

12 December 2020

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

1 reference

12 December 2020

The folding mechanism of a beta-sheet: the WW domain

1 reference

12 December 2020

Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

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12 December 2020

Cell division: AAAtacking the mitotic spindle

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7 January 2021

inferred from DOI database lookup

Peptide Folding: When Simulation Meets Experiment

1 reference

7 January 2021

inferred from DOI database lookup

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

1 reference

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NPHYS1713

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Dimensions Publication ID

2 August 2017

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2 August 2017

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