(Q35857030)

10 August 2017

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field (English)

1 reference

10 August 2017

0 references

3

William L Jorgensen

1 reference

10 August 2017

2

Julian Tirado-Rives

1 reference

10 August 2017

Michael J Robertson

1

1 reference

10 August 2017

1 June 2015

1 reference

Journal of Chemical Theory and Computation

10 August 2017

1 reference

10 August 2017

11

1 reference

10 August 2017

7

1 reference

10 August 2017

3499-3509

1 reference

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Perspectives on Basis Sets Beautiful: Seasonal Plantings of Diffuse Basis Functions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Residue-specific force field based on the protein coil library. RSFF1: modification of OPLS-AA/L.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Systematic validation of protein force fields against experimental data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

How fast-folding proteins fold

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Alchemical free energy methods for drug discovery: progress and challenges

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Influence of side chain conformations on local conformational features of amino acids and implication for force field development

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Efficient drug lead discovery and optimization

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Are current molecular dynamics force fields too helical?

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Crystallographic R factor refinement by molecular dynamics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Semiempirical hybrid density functional with perturbative second-order correlation

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Intrinsic backbone preferences are fully present in blocked amino acids

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Scalable molecular dynamics with NAMD

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Self-consistent Karplus parametrization of 3J couplings depending on the polypeptide side-chain torsion chi1.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Torsion angle dynamics for NMR structure calculation with the new program DYANA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Bayesian statistical analysis of protein side-chain rotamer preferences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Structure of ubiquitin refined at 1.8 A resolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

A Resolution-Of-The-Identity Implementation of the Local Triatomics-In-Molecules Model for Second-Order Møller-Plesset Perturbation Theory with Application to Alanine Tetrapeptide Conformational Energies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Effect of the damping function in dispersion corrected density functional theory.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Side-chain chi(1) conformations in urea-denatured ubiquitin and protein G from (3)J coupling constants and residual dipolar couplings

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Modern protein force fields behave comparably in molecular dynamics simulations

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

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

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4504185

Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings

14 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26190950

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

High-Level ab Initio Calculations To Improve Protein Backbone Dihedral Parameters

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26190950

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/ACS.JCTC.5B00356

1 reference

10 August 2017

1 reference

PMC publication ID

4504185

10 August 2017

PubMed publication ID

26190950

1 reference

PMC publication ID

4504185