(Q34125154)

31 July 2017

title

Combining optimal control theory and molecular dynamics for protein folding (English)

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31 July 2017

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Yaman Arkun

1

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31 July 2017

Mert Gur

series ordinal

2

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31 July 2017

language of work or name

English

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publication date

6 January 2012

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31 July 2017

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31 July 2017

volume

7

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31 July 2017

issue

1

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31 July 2017

page(s)

e29628

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Creative Commons Attribution 4.0 International

31 July 2017

copyright license

start time

6 January 2012

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Prediction of optimal folding routes of proteins that satisfy the principle of lowest entropy loss: dynamic contact maps and optimal control

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Common structural transitions in explicit-solvent simulations of villin headpiece folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Coarse-grained models of protein folding: toy models or predictive tools?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.

5 July 2018

1 reference

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Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back

5 July 2018

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A surprising simplicity to protein folding.

5 July 2018

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

5 July 2018

1 reference

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Theory of protein folding: the energy landscape perspective

5 July 2018

1 reference

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From Levinthal to pathways to funnels

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Essential dynamics of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Theoretical Studies of Protein Folding

5 July 2018

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Folding rates and low-entropy-loss routes of two-state proteins.

5 July 2018

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Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly.

21 January 2018

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Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems.

21 January 2018

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Folding dynamics of proteins from denatured to native state: principal component analysis.

21 January 2018

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Optimum folding pathways of proteins: their determination and properties.

21 January 2018

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Analysis of domain motions by approximate normal mode calculations.

21 January 2018

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Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure

21 January 2018

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Resolution exchange simulation.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3253094

Protein Folding Simulations: Combining Coarse-grained Models and All-atom Molecular Dynamics

28 October 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0029628

Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site

21 January 2018

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12 December 2020

Action-derived molecular dynamics in the study of rare events

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12 December 2020

A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells

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12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

All-atom fast protein folding simulations: the villin headpiece

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0029628

Identifiers

DOI

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31 July 2017

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31 July 2017

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