Elastic network normal modes provide a basis for protein structure refinement (Q30417014)

11 August 2017

Elastic network normal modes provide a basis for protein structure refinement (English)

1 reference

11 August 2017

0 references

3

Robert L Jernigan

1 reference

11 August 2017

4

Andrzej Kloczkowski

1 reference

11 August 2017

Andrzej Kolinski

2

0 references

Pawel Gniewek

series ordinal

1

object named as

Pawel Gniewek

1 reference

11 August 2017

PMC publication ID

3365912

language of work or name

English

0 references

publication date

1 May 2012

1 reference

Journal of Chemical Physics

11 August 2017

1 reference

11 August 2017

136

1 reference

11 August 2017

19

1 reference

11 August 2017

195101

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

The importance of slow motions for protein functional loops

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

How noise in force fields can affect the structural refinement of protein models?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Assessment of protein structure refinement in CASP9.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

I-TASSER: a unified platform for automated protein structure and function prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Global dynamics of proteins: bridging between structure and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

How significant is a protein structure similarity with TM-score = 0.5?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Normal mode analysis of biomolecular structures: functional mechanisms of membrane 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=3365912

Assessment of the protein-structure refinement category in CASP8

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

The energy profiles of atomic conformational transition intermediates of 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=3365912

FINDSITE: a threading-based approach to ligand homology modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

FINDSITE: a combined evolution/structure-based approach to protein function prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Solvent dramatically affects protein structure refinement.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

The protein folding problem

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Structural biology. Protein structure initiative: phase 3 or phase out.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

I-TASSER server for protein 3D structure prediction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Predicting the order in which contacts are broken during single molecule protein stretching experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

How well can we understand large-scale protein motions using normal modes of elastic network models?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Recent advances and applications of site-directed spin labeling.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Intrinsic dynamics of an enzyme underlies catalysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Rigid-cluster models of conformational transitions in macromolecular machines and assemblies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Scoring function for automated assessment of protein structure template quality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Protein modeling and structure prediction with a reduced representation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Critical assessment of methods of protein structure prediction (CASP)-round V.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Can correct protein models be identified?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Efficient generation of feasible pathways for protein conformational transitions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

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=3365912

Anisotropy of fluctuation dynamics of proteins with an elastic network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Identifying conformational changes with site-directed spin labeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Protein secondary structure prediction based on position-specific scoring matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Folding and binding cascades: shifts in energy landscapes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Clustering of low-energy conformations near the native structures of small 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=3365912

Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Theory of protein folding: the energy landscape perspective

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Molten globule and 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=3365912

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=3365912

Structural basis of hierarchical multiple substates of a protein. V: Nonlocal deformations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3365912

Hinge-bending motion in citrate synthase arising from normal mode calculations.

20 June 2018

1 reference

Computation of low-frequency normal modes in macromolecules: improvements to the method of diagonalization in a mixed basis and application to hemoglobin.

21 January 2018

1 reference

Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome

21 January 2018

1 reference

A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes.

21 January 2018

1 reference

HCPM--program for hierarchical clustering of protein models.

21 January 2018

1 reference

Anisotropic network model: systematic evaluation and a new web interface

21 January 2018

1 reference

Anharmonicity and Self-Similarity of the Free Energy Landscape of ProteinG

21 January 2018

1 reference

Approaching Elastic Network Models to Molecular Dynamics Flexibility

21 January 2018

1 reference

Elastic models of conformational transitions in macromolecules

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612113

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Immunoglobulin Structure Exhibits Control over CDR Motion

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612113

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Energy landscape of a native protein: jumping-among-minima model

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22612113

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.4710986

1 reference

11 August 2017

1 reference

PMC publication ID

3365912

11 August 2017

PubMed publication ID

22612113

1 reference

PMC publication ID

3365912