(Q30591583)

18 October 2017

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent (English)

1 reference

18 October 2017

0 references

1 reference

Hai Nguyen

1

1 reference

18 October 2017

James Maier

2

1 reference

18 October 2017

He Huang

3

1 reference

18 October 2017

Victoria Perrone

4

1 reference

18 October 2017

Carlos Simmerling

5

1 reference

18 October 2017

language of work or name

English

0 references

publication date

25 September 2014

1 reference

Journal of the American Chemical Society

18 October 2017

1 reference

18 October 2017

136

1 reference

18 October 2017

40

1 reference

18 October 2017

13959-13962

1 reference

Improved Generalized Born Solvent Model Parameters for Protein Simulations

18 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

RefSeq: an update on mammalian reference sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Atomic-level description of ubiquitin folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

The protein-folding problem, 50 years on.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Protein structure prediction from sequence variation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

How fast-folding proteins fold

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Rosetta in CASP4: progress in ab initio protein structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Ab initio protein structure prediction of CASP III targets using ROSETTA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4195377

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25255057

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JA5032776

1 reference

18 October 2017

1 reference

18 October 2017

PubMed publication ID

25255057

1 reference