Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation (Q37361318)

19 August 2017

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

1 reference

19 August 2017

Nikola Trbovic

1

1 reference

19 August 2017

Byungchan Kim

series ordinal

2

1 reference

19 August 2017

Richard A Friesner

series ordinal

3

1 reference

19 August 2017

Arthur G Palmer

series ordinal

4

1 reference

19 August 2017

language of work or name

English

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publication date

1 May 2008

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19 August 2017

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19 August 2017

71

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19 August 2017

2

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19 August 2017

684-694

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Improved sampling methods for molecular simulation

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

A consensus view of protein dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

New tools provide new insights in NMR studies of protein dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Do all backbone polar groups in proteins form hydrogen bonds?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Molecular dynamics and protein function

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Molecular dynamics and NMR spin relaxation in proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

An improved hydrogen bond potential: impact on medium resolution protein structures.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Calculations of NMR dipolar coupling strengths in model peptides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Dynamics of folded proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2750878

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

2 September 2018

1 reference

12 December 2020

NMR characterization of the dynamics of biomacromolecules

1 reference

12 December 2020

Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins

1 reference

12 December 2020

Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results

1 reference

12 December 2020

Hydrogen bonds in molecular mechanics force fields

1 reference

12 December 2020

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

1 reference

12 December 2020

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

1 reference

12 December 2020

Backbone motions of free and pheromone-bound major urinary protein I studied by molecular dynamics simulation

1 reference

12 December 2020

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.21750

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

17975832

1 reference