Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements (Q34285601)

1 August 2017

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements (English)

1 reference

1 August 2017

computational benchmark

1 reference

Yu-Shan Lin

2

0 references

Rhiju Das

object named as

Rhiju Das

series ordinal

3

0 references

Vijay Pande

series ordinal

4

object named as

Vijay S Pande

1 reference

1 August 2017

1

Kyle A Beauchamp

1 reference

1 August 2017

12 March 2012

1 reference

Journal of Chemical Theory and Computation

1 August 2017

1 reference

1 August 2017

8

1 reference

1 August 2017

4

1 reference

1 August 2017

1409-1414

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

OpenMM: A Hardware Independent Framework for Molecular Simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Populations of the three major backbone conformations in 19 amino acid dipeptides.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Atomic-level characterization of the structural dynamics of proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Predicting absolute ligand binding free energies to a simple model site

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Canonical sampling through velocity rescaling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Intrinsic backbone preferences are fully present in blocked amino acids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

A general purpose model for the condensed phases of water: TIP4P/2005

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Exploring protein native states and large-scale conformational changes with a modified generalized born model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Knowledge-based protein secondary structure assignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Structure of ubiquitin refined at 1.8 A resolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Improved treatment of the protein backbone in empirical force fields.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383641

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22754404

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Distinguishing between two-state and three-state models for ubiquitin folding

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22754404

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT2007814

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

PubMed ID

22754404