(Q42853031)

8 November 2017

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

1 reference

8 November 2017

0 references

1 reference

Kresten Lindorff-Larsen

series ordinal

2

1 reference

8 November 2017

Stefano Piana

1

1 reference

8 November 2017

David E Shaw

series ordinal

3

1 reference

8 November 2017

language of work or name

English

0 references

publication date

1 May 2011

1 reference

8 November 2017

1 reference

8 November 2017

100

1 reference

8 November 2017

9

1 reference

8 November 2017

L47-9

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

8 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Computational design and experimental testing of the fastest-folding β-sheet protein

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Atomic-level characterization of the structural dynamics of proteins

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Long-timescale molecular dynamics simulations of protein structure and function.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Are current molecular dynamics force fields too helical?

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Sub-microsecond protein folding

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Unifying features in protein-folding mechanisms

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Absolute comparison of simulated and experimental protein-folding dynamics

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Knowledge-based protein secondary structure assignment

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3149239

10.1016/J.BPJ.2011.03.051

16 August 2018

Identifiers

DOI

1 reference

8 November 2017

1 reference

8 November 2017

PubMed publication ID

21539772

1 reference