(Q36930272)

English

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems

scientific article published on July 2005

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems (English)

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

Harold A. Scheraga

4

object named as

Harold A Scheraga

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

2

object named as

Adam Liwo

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

author name string

Mey Khalili

1

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

Anna Jagielska

3

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

language of work or name

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publication date

1 July 2005

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

109

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

28

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

13798-13810

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

1 reference

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29 September 2017

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

1 reference

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29 September 2017

Deterministic and stochastic algorithms for mechanical systems under constraints.

1 reference

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29 September 2017

The protein folding 'speed limit'.

1 reference

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29 September 2017

Testing protein-folding simulations by experiment: B domain of protein A.

1 reference

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29 September 2017

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

1 reference

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29 September 2017

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field

1 reference

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29 September 2017

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

1 reference

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29 September 2017

Recent improvements in prediction of protein structure by global optimization of a potential energy function.

1 reference

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29 September 2017

Generalized born models of macromolecular solvation effects

1 reference

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29 September 2017

Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Protein structure prediction by global optimization of a potential energy function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Exploring the folding free energy surface of a three-helix bundle protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Absence of a stable intermediate on the folding pathway of protein A.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Prediction of protein conformation on the basis of a search for compact structures: test on avian pancreatic polypeptide

1 reference

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29 September 2017

Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

29 September 2017

Atomic solvation parameters applied to molecular dynamics of proteins in solution

1 reference

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29 September 2017

A simplified representation of protein conformations for rapid simulation of protein folding

1 reference

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29 September 2017

Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect

1 reference

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27 June 2018

Computing time scales from reaction coordinates by milestoning.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

4 September 2018

Addition of side chains to a known backbone with defined side-chain centroids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2564622

4 September 2018

Protein folding simulation with solvent-induced force field: folding pathway ensemble of three-helix-bundle proteins

1 reference

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20 October 2018

Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermal folding and mechanical unfolding pathways of protein secondary structures

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

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Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

An all atom force field for simulations of proteins and nucleic acids

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

1 reference

https://pubmed.ncbi.nlm.nih.gov/16852728

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JP058007W

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

17 August 2017

ResearchGate publication ID

0 references

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