(Q41142772)

27 September 2017

Features of large hinge-bending conformational transitions. Prediction of closed structure from open state (English)

1 reference

27 September 2017

4

Pemra Doruker

1 reference

27 September 2017

3

Turkan Haliloglu

1 reference

27 September 2017

Arzu Uyar

1

1 reference

27 September 2017

Nigar Kantarci-Carsibasi

series ordinal

2

1 reference

27 September 2017

language of work or name

English

0 references

publication date

1 June 2014

1 reference

27 September 2017

1 reference

27 September 2017

106

1 reference

27 September 2017

12

1 reference

27 September 2017

2656-2666

1 reference

Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Conformational transitions upon ligand binding: holo-structure prediction from apo conformations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

The energy profiles of atomic conformational transition intermediates of adenylate kinase

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Conformational transitions of adenylate kinase: switching by cracking

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Coarse-grained normal mode analysis in structural biology

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Efficient generation of feasible pathways for protein conformational transitions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

ATP-bound states of GroEL captured by cryo-electron microscopy

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Anisotropy of fluctuation dynamics of proteins with an elastic network model

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

A new method for modeling large-scale rearrangements of protein domains

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

SCOP: a structural classification of proteins database for the investigation of sequences and structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Heterogeneous path ensembles for conformational transitions in semi-atomistic models of adenylate kinase

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Molecular dynamics of apo-adenylate kinase: a principal component analysis

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Conformational change of proteins arising from normal mode calculations

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

The blind search for the closed states of hinge-bending proteins.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Geometry-based sampling of conformational transitions in proteins.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Protein conformational transitions explored by mixed elastic network models.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4070069

Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures

19 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24940783

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24940783

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2014.05.017

1 reference

27 September 2017

1 reference

27 September 2017

PubMed publication ID

24940783

1 reference