(Q26822885)

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Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

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Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations (English)

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molecular dynamics simulation

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protein folding

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author name string

Stefano Piana

1

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John L Klepeis

2

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David E Shaw

3

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language of work or name

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publication date

February 2014

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Current Opinion in Structural Biology

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24

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98-105

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On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

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inferred from DOI database lookup

CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data

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7 January 2021

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

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7 January 2021

based on heuristic

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Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

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7 January 2021

based on heuristic

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Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

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7 January 2021

based on heuristic

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Temperature and pressure denaturation of chignolin: folding and unfolding simulation by multibaric-multithermal molecular dynamics method

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7 January 2021

based on heuristic

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Folding of Top7 in unbiased all-atom Monte Carlo simulations.

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7 January 2021

based on heuristic

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How to derive a protein folding potential? A new approach to an old problem

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Comparison of protein force fields for molecular dynamics simulations

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

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Enhanced sampling algorithms

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Contact potential that recognizes the correct folding of globular proteins

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Force field bias in protein folding simulations

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7 January 2021

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Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

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7 January 2021

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Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water

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7 January 2021

based on heuristic

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

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Three force fields' views of the 3(10) helix.

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7 January 2021

based on heuristic

inferred from DOI database lookup

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

1 reference

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7 January 2021

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Discerning the structure and energy of multiple transition states in protein folding using psi-analysis

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Early collapse is not an obligate step in protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Sub-microsecond protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

The folding mechanism of BBL: Plasticity of transition-state structure observed within an ultrafast folding protein family

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Theory of protein folding

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Transition networks for modeling the kinetics of conformational change in macromolecules

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Targeting biomolecular flexibility with metadynamics

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

How, when and why proteins collapse: the relation to folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Atomistic molecular simulations of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Rapid Cooperative Two-state Folding of a Miniature α–β Protein and Design of a Thermostable Variant

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Pathways for protein folding: is a new view needed?

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Is there a unifying mechanism for protein folding?

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Calorimetric analysis of lambda cI repressor binding to DNA operator sites

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Reversible dimerization of acid-denatured ACBP controlled by helix A4.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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The Native GCN4 Leucine-Zipper Domain Does Not Uniquely Specify a Dimeric Oligomerization State

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Probing the folding transition state of ubiquitin mutants by temperature-jump-induced downhill unfolding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Thermodynamic characterization of the folding equilibrium of the human Nedd4-WW4 domain: at the frontiers of cooperative folding.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Crystal structure of a ten-amino acid protein

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Unfolded-state dynamics and structure of protein L characterized by simulation and experiment

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Folding simulations of the A and B domains of protein G

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Confinement-induced states in the folding landscape of the Trp-cage miniprotein

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Atomistic description of the folding of a dimeric protein

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Computer simulation of protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Mapping the transition state and pathway of protein folding by protein engineering

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Atom-by-atom analysis of global downhill protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Behind the folding funnel diagram

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

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Capturing the essence of folding and functions of biomolecules using coarse-grained models

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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On developing coarse-grained models for biomolecular simulation: a review

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based on heuristic

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Microsecond folding experiments and simulations: a match is made

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

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A general purpose model for the condensed phases of water: TIP4P/2005

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

The relative helix and hydrogen bond stability in the B domain of protein A as revealed by integrated tempering sampling molecular dynamics simulation

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Canonical and micro-canonical analysis of folding of trpzip2: an all-atom replica exchange Monte Carlo simulation study.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein.

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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Random-coil behavior and the dimensions of chemically unfolded proteins

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Phi-value analysis by molecular dynamics simulations of reversible folding

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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From the Cover: Charge interactions can dominate the dimensions of intrinsically disordered proteins.

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Folding helical proteins in explicit solvent using dihedral-biased tempering

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Energy landscape of knotted protein folding

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Protein folding kinetics and thermodynamics from atomistic simulation

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

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De novo prediction of protein folding pathways and structure using the principle of sequential stabilization

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Atomic-level description of ubiquitin folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Folding simulations of a three-stranded antiparallel beta -sheet peptide

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Optimal protein-folding codes from spin-glass theory

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

The Trp-cage: optimizing the stability of a globular miniprotein

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Folding and association of a homotetrameric protein complex in an all-atom Go model

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Simplified protein models: predicting folding pathways and structure using amino acid sequences.

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Contact order revisited: influence of protein size on the folding rate

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

A unified mechanism for protein folding: predetermined pathways with optional errors

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Atomic-level characterization of the structural dynamics of proteins

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

How fast-folding proteins fold

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

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inferred from DOI database lookup

Single-molecule fluorescence experiments determine protein folding transition path times

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Folding pathways of a knotted protein with a realistic atomistic force field

1 reference

https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

The energy computation paradox and ab initio protein folding

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Systematic validation of protein force fields against experimental data

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

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https://api.crossref.org/works/10.1016%2FJ.SBI.2013.12.006

7 January 2021

based on heuristic

inferred from DOI database lookup

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

1 reference

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7 January 2021

based on heuristic

inferred from DOI database lookup

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