(Q30477971)

16 November 2017

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations (English)

1 reference

molecular dynamics simulation

16 November 2017

0 references

1 reference

Kei-ichi Okazaki

0 references

Peter G Wolynes

1 reference

16 November 2017

Nobuyasu Koga

1 reference

16 November 2017

Shoji Takada

series ordinal

1 reference

16 November 2017

Jose N Onuchic

series ordinal

1 reference

16 November 2017

language of work or name

English

0 references

publication date

28 July 2006

1 reference

Proceedings of the National Academy of Sciences of the United States of America

16 November 2017

1 reference

16 November 2017

103

1 reference

16 November 2017

1 reference

16 November 2017

11844-11849

1 reference

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

16 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Coarse-grained models for proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Conformational change of proteins arising from normal mode calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Go-ing for the prediction of protein folding mechanisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Stretching lattice models of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

A database of macromolecular motions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Structural correlations in protein folding funnels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Funnels, pathways, and the energy landscape of protein folding: a synthesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Theoretical Studies of Protein Folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Rate theories and puzzles of hemeprotein kinetics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Protein states and proteinquakes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Spin glasses and the statistical mechanics of protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

The nature of folded states of globular proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Protein folding funnels: a kinetic approach to the sequence-structure relationship

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1567665

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

20 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Simple energy landscape model for the kinetics of functional transitions in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Combining prediction, computation and experiment for the characterization of protein disorder

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Electron transfers in chemistry and biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

The hinge-bending mode in lysozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0604375103

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16877541

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein structural change upon ligand binding: linear response theory

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16877541

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0604375103

1 reference

16 November 2017

0 references

1 reference

16 November 2017

PubMed publication ID

16877541

1 reference