(Q36799132)

16 August 2017

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

1 reference

16 August 2017

1 reference

Carlo Camilloni

2

0 references

Alessandro Laio

object named as

Alessandro Laio

series ordinal

4

0 references

Michele Vendruscolo

series ordinal

3

object named as

Michele Vendruscolo

1 reference

16 August 2017

Daniele Granata

1

1 reference

16 August 2017

language of work or name

English

0 references

publication date

9 April 2013

1 reference

Proceedings of the National Academy of Sciences of the United States of America

16 August 2017

1 reference

16 August 2017

110

1 reference

16 August 2017

17

1 reference

16 August 2017

6817-6822

1 reference

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

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Genomics-aided structure prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Structure of an intermediate state in protein folding and aggregation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Atomistic molecular simulations of protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

How fast-folding proteins fold

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

SHIFTX2: significantly improved protein chemical shift prediction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Atomic-level characterization of the structural dynamics of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

COMPUTING: Screen Savers of the World Unite!

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

A bias-exchange approach to protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Simultaneous determination of protein structure and dynamics.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Determination of a transition state at atomic resolution from protein engineering data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Escaping free-energy minima

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Molecular dynamics simulations of biomolecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Molecular dynamics simulations of protein folding from the transition state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Protein folding and unfolding at atomic resolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Development and current status of the CHARMM force field for nucleic acids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Three key residues form a critical contact network in a protein folding transition state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

A simple model for calculating the kinetics of protein folding from three-dimensional structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Canonical dynamics: Equilibrium phase-space distributions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

An early intermediate in the folding reaction of the B1 domain of protein G contains a native-like core

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

From Levinthal to pathways to funnels

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

VMD: visual molecular dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Navigating the folding routes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Folding of Protein G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure Elements

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

The Energy Landscapes and Motions of Proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Exploring the protein G helix free-energy surface by solute tempering metadynamics.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Critical role of beta-hairpin formation in protein G folding.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3637744

Protein Folding: A Perspective from Theory and Experiment.

5 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

Equilibrium Free Energies from Nonequilibrium Metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

Protein Folding and Ligand-Enzyme Binding from Bias-Exchange Metadynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1218350110

21 January 2018

Identifiers

DOI

10.1073/PNAS.1218350110

1 reference

release_ufu5hld6fre7tho3zqjjtlrpo4

16 August 2017

0 references

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ufu5hld6fre7tho3zqjjtlrpo4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

16 August 2017

PubMed publication ID

23572592

1 reference