(Q41808112)

12 October 2017

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape (English)

1 reference

12 October 2017

1 reference

3

Sebastian Doniach

1 reference

12 October 2017

Patrice Koehl

2

0 references

author name string

Joel Franklin

series ordinal

1

1 reference

PMCID

1933200

12 October 2017

Marc Delarue

series ordinal

4

1 reference

12 October 2017

1 June 2007

1 reference

12 October 2017

Nucleic Acids Research

1 reference

12 October 2017

35

1 reference

12 October 2017

W477-82

1 reference

12 October 2017

Web Server issue

1 reference

The dynamic energy landscape of dihydrofolate reductase catalysis

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

The Database of Macromolecular Motions: new features added at the decade mark

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Quantifying kinetic paths of protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Atomically Detailed Simulations of Helix Formation with the Stochastic Difference Equation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Small libraries of protein fragments model native protein structures accurately.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Efficient generation of feasible pathways for protein conformational transitions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

An atomically detailed study of the folding pathways of protein A with the stochastic difference equation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Conformational change of proteins arising from normal mode calculations

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Theoretical Studies of Protein Folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Dominant pathways in protein folding.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Anisotropic network model: systematic evaluation and a new web interface.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

Analysis of domain motions by approximate normal mode calculations.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

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

2 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933200

2 December 2018

Identifiers

DOI

10.1093/NAR/GKM342

1 reference

journals/nar/FranklinKDD07

12 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

12 October 2017

1 reference

PMCID

1933200