A test on peptide stability of AMBER force fields with implicit solvation (Q30369376)

19 August 2017

A test on peptide stability of AMBER force fields with implicit solvation (English)

1 reference

19 August 2017

0 references

3

Ken A Dill

1 reference

19 August 2017

M Scott Shell

1

1 reference

PMCID

2699260

19 August 2017

Ryan Ritterson

series ordinal

2

1 reference

PMCID

2699260

19 August 2017

language of work or name

English

0 references

publication date

10 May 2008

1 reference

Journal of Physical Chemistry B

19 August 2017

1 reference

19 August 2017

112

1 reference

19 August 2017

22

1 reference

19 August 2017

6878-6886

1 reference

Generalized Born model with a simple, robust molecular volume correction

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Protein folding by zipping and assembly

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Two-stage folding of HP-35 from ab initio simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Force field influences in beta-hairpin folding simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

The Amber biomolecular simulation programs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Effective Born radii in the generalized Born approximation: the importance of being perfect

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Tryptophan zippers: Stable, monomeric -hairpins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Generalized born models of macromolecular solvation effects

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

VMD: visual molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Urea unfolding of peptide helices as a model for interpreting protein unfolding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

A salt bridge stabilizes the helix formed by isolated C-peptide of RNase A

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Solvation energy in protein folding and binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Is Poisson-Boltzmann theory insufficient for protein folding simulations?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2699260

Theory and applications of the generalized Born solvation model in macromolecular simulations

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18471007

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18471007

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18471007

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JP800282X

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

PMCID

2699260