Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data (Q33636214)

28 July 2017

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data (English)

1 reference

28 July 2017

2

David van der Spoel

1 reference

28 July 2017

Oliver F Lange

1

1 reference

PubMed ID

20643085

28 July 2017

Bert L de Groot

series ordinal

3

1 reference

PubMed ID

20643085

28 July 2017

language of work or name

English

0 references

publication date

1 July 2010

1 reference

28 July 2017

9

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

28 July 2017

99

1 reference

28 July 2017

2

1 reference

28 July 2017

647-655

1 reference

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

28 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Toward a unified representation of protein structural dynamics in solution.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Are current molecular dynamics force fields too helical?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of 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=2905107

Effects of long-range electrostatic forces on simulated protein folding kinetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Simultaneous definition of high resolution protein structure and backbone conformational dynamics using NMR residual dipolar couplings.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Correlation of protein structure and dynamics to scalar couplings across 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=2905107

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of 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=2905107

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=2905107

NMR residual dipolar couplings as probes of biomolecular 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=2905107

Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Protein structure prediction using Rosetta

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

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=2905107

A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Scalar couplings across 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=2905107

How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Essential dynamics of 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=2905107

Influence of Long-Range Electrostatic Treatments on the Folding of the N-Terminal H4 Histone Tail Peptide.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Composite alignment media for the measurement of independent sets of NMR residual dipolar couplings.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Orientation restraints in molecular dynamics simulations using time and ensemble averaging

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

A DFT study of the interresidue dependencies of scalar J-coupling and magnetic shielding in the hydrogen-bonding regions of a DNA triplex.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Direct Observation of Cα−Hα···OC Hydrogen Bonds in Proteins by Interresidueh3JCαC‘Scalar Couplings

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2905107

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

10 December 2018

1 reference

12 December 2020

The Origin of Layer Structure Artifacts in Simulations of Liquid Water

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

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

1 reference

12 December 2020

NMR characterization of the dynamics of biomacromolecules

1 reference

12 December 2020

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

1 reference

12 December 2020

Direct Comparison of Experimental and Calculated NMR Scalar Coupling Constants for Force Field Validation and Adaptation

1 reference

12 December 2020

Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings

1 reference

12 December 2020

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal

1 reference

12 December 2020

10.1016/J.BPJ.2010.04.062

Identifiers

DOI

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

PubMed ID

20643085