(Q34649543)

3 August 2017

title

Folding pathways of a knotted protein with a realistic atomistic force field (English)

1 reference

3 August 2017

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5

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Roberto Covino

object named as

Roberto Covino

3

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author name string

Silvio a Beccara

1

1 reference

3 August 2017

Tatjana Škrbić

2

1 reference

3 August 2017

Cristian Micheletti

4

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3 August 2017

language of work or name

1 reference

21 March 2013

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PLOS Computational Biology

3 August 2017

published in

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3 August 2017

volume

9

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3 August 2017

issue

3

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3 August 2017

page(s)

e1003002

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Creative Commons Attribution 4.0 International

3 August 2017

copyright license

start time

21 March 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Energy landscape of knotted protein folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

The role of non-native interactions in the folding of knotted proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Dominant folding pathways of a WW domain.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Structures and folding pathways of topologically knotted proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Structure and folding of a designed knotted protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Atomic-level characterization of the structural dynamics of proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Slipknotting upon native-like loop formation in a trefoil knot protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Knotted vs. unknotted proteins: evidence of knot-promoting loops

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

A Stevedore's protein knot

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Coordinate-dependent diffusion in protein folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Dodging the crisis of folding proteins with knots

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

How does a knotted protein fold?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Knotted and topologically complex proteins as models for studying folding and stability

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Protein knots and fold complexity: some new twists.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

The folding mechanics of a knotted protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Statistics of knots, geometry of conformations, and evolution of proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

VMD: visual molecular dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Refined structure of human carbonic anhydrase II at 2.0 A resolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Are there knots in proteins?

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

Dominant pathways in protein folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

Dominant reaction pathways in high-dimensional systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

The free energy landscape analysis of protein (FIP35) folding dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

Multiscale entanglement in ring polymers under spherical confinement.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003002

Fast Monte Carlo algorithms for knotted polymers.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3605060

Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23555232

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Quantitative protein dynamics from dominant folding pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23555232

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Fluctuations in the ensemble of reaction pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23555232

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003002

1 reference

journals/ploscb/BeccaraSCMF13

3 August 2017

1 reference

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

3 August 2017

1 reference