(Q39110778)

9 September 2017

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

1 reference

9 September 2017

1 reference

4

David A Case

0 references

author name string

David S Cerutti

1

1 reference

9 September 2017

William C Swope

2

1 reference

9 September 2017

Julia E Rice

3

1 reference

9 September 2017

David A Case

4

1 reference

9 September 2017

18 September 2014

1 reference

Journal of Chemical Theory and Computation

9 September 2017

1 reference

9 September 2017

10

1 reference

9 September 2017

10

1 reference

9 September 2017

4515-4534

1 reference

Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Evaluating the strength of salt bridges: a comparison of current biomolecular force fields

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

A numerically stable restrained electrostatic potential charge fitting method

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Are current molecular dynamics force fields too helical?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

The Amber biomolecular simulation programs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

10 residue folded peptide designed by segment statistics.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Empirical force fields for biological macromolecules: overview and issues.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Designing a 20-residue protein

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Refinement of triclinic hen egg-white lysozyme at atomic resolution

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Folding dynamics and mechanism of beta-hairpin formation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Electronic Polarizability and the Effective Pair Potentials of Water

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Design and characterization of helical peptides that inhibit the E6 protein of papillomavirus

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4196740

Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus

2 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25328495

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Role of side-chains in the cooperative beta-hairpin folding of the short C-terminal fragment derived from streptococcal protein G

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25328495

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT500643C

1 reference

release_nuevgf2gyfaubpvok55jpcqum4

9 September 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/nuevgf2gyfaubpvok55jpcqum4

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

9 September 2017

PubMed publication ID

25328495

1 reference