(Q36838938)

16 August 2017

Exploring the suitability of coarse-grained techniques for the representation of protein dynamics (English)

1 reference

16 August 2017

Oliver Carrillo

2

0 references

Modesto Orozco

series ordinal

4

object named as

Modesto Orozco

1 reference

16 August 2017

Agustí Emperador

1

1 reference

PMCID

2517050

16 August 2017

Manuel Rueda

series ordinal

3

1 reference

PMCID

2517050

16 August 2017

language of work or name

English

0 references

publication date

16 May 2008

1 reference

16 August 2017

12

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

16 August 2017

95

1 reference

16 August 2017

2127-2138

1 reference

16 August 2017

5

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

A consensus view of protein dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Side-chain interactions determine amyloid formation by model polyglutamine peptides in molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Data mining of molecular dynamics trajectories of nucleic acids

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Scalable molecular dynamics with NAMD

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Molecular dynamics and protein function

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Simultaneous determination of protein structure and dynamics.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Theoretical methods for the simulation of nucleic acids.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Mechanism for the alpha-helix to beta-hairpin transition

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

A consensus view of fold space: Combining SCOP, CATH, and the Dali Domain Dictionary

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

The role of dynamics in enzyme activity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Molecular dynamics simulations of biomolecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Enzyme dynamics during catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Essential dynamics of proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Bicycle-pedal model for the first step in the vision process

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Dynamics of folded proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Investigating the local flexibility of functional residues in hemoproteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Multiscale modeling of nucleosome dynamics

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Predictions of protein flexibility: first-order measures

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Discrete molecular dynamics simulations of peptide aggregation.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Analysis of domain motions by approximate normal mode calculations.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Interpreting the folding kinetics of helical proteins

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2517050

Analysis of domain motions in large proteins

4 December 2018

1 reference

12 December 2020

1 reference

12 December 2020

Stabilization of Proteins by Ligand Binding: Application to Drug Screening and Determination of Unfolding Energetics

1 reference

12 December 2020

Exploring the Essential Dynamics of B-DNA

1 reference

12 December 2020

The dynamics of proteins

1 reference

12 December 2020

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study

1 reference

12 December 2020

Erythropoietin receptor activation by a ligand-induced conformation change

1 reference

12 December 2020

10.1529/BIOPHYSJ.107.119115

Identifiers

DOI

1 reference

16 August 2017

1 reference

16 August 2017

1 reference

PMCID

2517050