Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics (Q27335812)

April 2022 Public Data File from Crossref

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A novel switch region regulates H-ras membrane orientation and signal output

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

The structural basis for the transition from Ras-GTP to Ras-GDP

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Dynamic properties of the Ras switch I region and its importance for binding to effectors

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

The Amber biomolecular simulation programs

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

The guanine nucleotide-binding switch in three dimensions

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Ras plasma membrane signalling platforms

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Ras oncogenes: split personalities

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Structure-function based design of small molecule inhibitors targeting Rho family GTPases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

H-ras, K-ras, and inner plasma membrane raft proteins operate in nanoclusters with differential dependence on the actin cytoskeleton

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Structure of the metal-water complex in Ras x GDP studied by high-field EPR spectroscopy and 31P NMR spectroscopy

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

GTP-dependent segregation of H-ras from lipid rafts is required for biological 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=2651530

Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Domain communication in the dynamical structure of human immunodeficiency virus 1 protease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Conformational change of proteins arising from normal mode calculations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Calculation of pathways for the conformational transition between the GTP‐ and GDP‐bound states of the Ha‐ras‐p21 protein: Calculations with explicit solvent simulations and comparison with calculations in vacuum

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

Structure of the G60A mutant of Ras: implications for the dominant negative effect

2 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Structure of a transient intermediate for GTP hydrolysis by ras.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: flexibility, possible hinges, and levers of the conformational transition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Sampling of slow diffusive conformational transitions with accelerated molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Development of polyphosphate parameters for use with the AMBER force field.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Bio3d: an R package for the comparative analysis of protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Simulation of the solution structure of the H-ras p21-GTP complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PCBI.1000325

Building-block approach for determining low-frequency normal modes of macromolecules

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2651530

10.1371/JOURNAL.PCBI.1000325

27 November 2018

Identifiers

DOI

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journals/ploscb/GrantGM09

DBLP publication ID

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DBLP Dataset 2021-01-02

28 January 2021

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1 reference

PubMed publication ID

19300489

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