Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids (Q28353933)

on focus list of Wikimedia project

volume

3

0 references

page(s)

85

0 references

WikiProject Zika Corpus

0 references

cites work

Structure of the thermally stable Zika virus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The 3.8 Å resolution cryo-EM structure of Zika virus

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Near-Atomic Resolution Cryo-Electron Microscopic Structure of Dengue Serotype 4 Virus

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Immature and Mature Dengue Serotype 1 Virus Structures Provide Insight into the Maturation Process

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Structural Changes in Dengue Virus When Exposed to a Temperature of 37 C

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The global distribution and burden of dengue

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Cryo-EM structure of the mature dengue virus at 3.5-Å resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The structural basis for serotype-specific neutralization of dengue virus by a human antibody

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Structural proteomics of dengue virus

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

A ligand-binding pocket in the dengue virus envelope glycoprotein

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

XFELs open a new era in structural chemical biology

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The renormalization group: Critical phenomena and the Kondo problem

20 March 2017

1 reference

https://api.crossref.org/works/10.3389/FMOLB.2016.00085

Conformational changes of the flavivirus E glycoprotein

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Coarse-Grained Protein Models and Their Applications

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

New generation of elastic network models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Robust Heterogeneous Anisotropic Elastic Network Model Precisely Reproduces the Experimental B-factors 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=5187361

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Unstructural biology of the Dengue virus 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=5187361

A comparison of weighted ensemble and Markov state model methodologies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Mathematics's role in the grand challenge of deciphering the molecular basis of life

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface 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=5187361

The anisotropic network model web server at 2015 (ANM 2.0).

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

On the relationship between low-frequency normal modes and the large-scale conformational changes 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=5187361

WEBnm@ v2.0: Web server and services for comparing protein flexibility

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Systematic methods for defining coarse-grained maps in large 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=5187361

Identifying essential pairwise interactions in elastic network model using the alpha shape theory.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Coarse-graining methods for computational biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Elastic Network Models are Robust to Variations in Formalism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Refining the global spatial limits of dengue virus transmission by evidence-based consensus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

On developing coarse-grained models for biomolecular simulation: a review

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in 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=5187361

Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained 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=5187361

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network 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=5187361

Protein elastic network models and the ranges of cooperativity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

A systematic methodology for defining coarse-grained sites in large 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=5187361

Dengue and hemorrhagic fever: a potential threat to public health in the United States

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The gaussian network model: precise prediction of residue fluctuations and application to binding problems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Can conformational change be described by only a few normal modes?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Coarse-grained models for 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=5187361

A comparative study of motor-protein motions by using a simple elastic-network 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=5187361

Efficient generation of feasible pathways for protein conformational transitions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Dynamics of proteins in crystals: comparison of experiment with simple models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Anisotropy of fluctuation dynamics of proteins with an elastic network 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=5187361

Computer simulation of protein folding

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

An elastic network model of HK97 capsid maturation

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Conformational change of proteins arising from normal mode calculations

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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=5187361

Normal modes of symmetric protein assemblies. Application to the tobacco mosaic virus protein disk

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

2 June 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Eigenvalue computation in the 20th century

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Analysis of domain motions by approximate normal mode calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Predictions of protein flexibility: first-order measures

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Group theory of icosahedral virus capsid vibrations: a top-down approach

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Maturation dynamics of bacteriophage HK97 capsid

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

The geometric minimum action method for computing minimum energy paths.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Adaptive minimum action method for the study of rare events.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Approaching Elastic Network Models to Molecular Dynamics Flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

A new algorithm for construction of coarse-grained sites of large biomolecules.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

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

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5187361

Collective variable description of small-amplitude conformational fluctuations in a globular protein

27 November 2018

1 reference

https://api.crossref.org/works/10.3389%2FFMOLB.2016.00085

Allostery in a coarse-grained model of protein dynamics

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28083537

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28083537