(Q30577861)

13 October 2017

Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters (English)

1 reference

13 October 2017

1 reference

Tim Zeiske

1

1 reference

13 October 2017

Kate A Stafford

series ordinal

2

1 reference

13 October 2017

Richard A Friesner

series ordinal

3

1 reference

13 October 2017

Arthur G Palmer

series ordinal

4

1 reference

13 October 2017

language of work or name

English

0 references

publication date

24 December 2012

1 reference

13 October 2017

1 reference

13 October 2017

81

1 reference

13 October 2017

3

1 reference

13 October 2017

499-509

1 reference

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Site-specific backbone amide (15)N chemical shift anisotropy tensors in a small protein from liquid crystal and cross-correlated relaxation measurements

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Are current molecular dynamics force fields too helical?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Computational techniques for efficient conformational sampling of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Improved sampling methods for molecular simulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

An assessment of the accuracy of methods for predicting hydrogen positions in protein structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Long-timescale simulation methods

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Generalized-ensemble algorithms for molecular simulations of biopolymers

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Calculations of NMR dipolar coupling strengths in model peptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

VMD: visual molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Simulated annealing approach to the study of protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3557728

Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

Model-Free Approach to the Dynamic Interpretation of Residual Dipolar Couplings in Globular Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

Force Field Validation Using Protein Side Chain Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24209

Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23161667

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

NMR characterization of the dynamics of biomacromolecules

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23161667

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/PROT.24209

1 reference

13 October 2017

1 reference

13 October 2017

PubMed publication ID

23161667

1 reference