(Q31154422)

15 August 2017

Are current molecular dynamics force fields too helical? (English)

1 reference

molecular dynamics simulation

15 August 2017

0 references

Robert B Best

1

0 references

Gerhard Hummer

object named as

Gerhard Hummer

series ordinal

3

0 references

author name string

Nicolae-Viorel Buchete

series ordinal

2

1 reference

PMC publication ID

2426634

15 August 2017

language of work or name

English

0 references

publication date

2 May 2008

1 reference

15 August 2017

1 reference

15 August 2017

95

1 reference

15 August 2017

1

1 reference

15 August 2017

L07-9

1 reference

Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Conformation of the backbone in unfolded proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Polyproline II conformation is one of many local conformational states and is not an overall conformation of unfolded peptides and proteins.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Simultaneous determination of protein structure and dynamics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Empirical force fields for biological macromolecules: overview and issues.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Molecular dynamics simulations of biomolecules

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Peptide folding kinetics from replica exchange molecular dynamics.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Coarse master equations for peptide folding dynamics.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Combining prediction, computation and experiment for the characterization of protein disorder.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Improved treatment of the protein backbone in empirical force fields.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Elucidating the folding problem of helical peptides using empirical parameters

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2426634

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18456823

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18456823

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18456823

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1529/BIOPHYSJ.108.132696

1 reference

15 August 2017

1 reference

PMC publication ID

2426634

15 August 2017

PubMed publication ID

18456823

1 reference

PMC publication ID

2426634