(Q37263082)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

title

An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

main subject

protein folding

0 references

computational benchmark

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

author name string

Sanbo Qin

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

language of work or name

1 reference

1 October 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

29 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

issue

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

Folding free energy surfaces of three small proteins under crowding: validation of the postprocessing method by direct simulation

29 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Simulation and Modeling of Crowding Effects on the Thermodynamic and Kinetic Properties of Proteins with Atomic Details

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Influence of crowded cellular environments on protein folding, binding, and oligomerization: biological consequences and potentials of atomistic modeling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Modulation of functionally significant conformational equilibria in adenylate kinase by high concentrations of trimethylamine oxide attributed to volume exclusion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Effects of macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Attractive protein-polymer interactions markedly alter the effect of macromolecular crowding on protein association equilibria.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Effects of macromolecular crowding on protein conformational changes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Generalized fundamental measure theory for atomistic modeling of macromolecular crowding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Dependence of protein folding stability and dynamics on the density and composition of macromolecular crowders

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Effect of macromolecular crowding on protein binding stability: modest stabilization and significant biological consequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Prediction of protein solubility from calculation of transfer free energy

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

A pseudopotential for improving the packing of ellipsoidal protein structures determined from NMR data.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Molecular crowding enhances native state stability and refolding rates of globular proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Influence of molecular configuration on the passage of macromolecules across the glomerular capillary wall

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Method to Predict Crowding Effects by Postprocessing Molecular Dynamics Trajectories: Application to the Flap Dynamics of HIV-1 Protease.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Nonadditive effects of mixed crowding on protein stability

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

The influence of macromolecular crowding on HIV-1 protease internal dynamics

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Thermodynamic nonideality in macromolecular solutions: interpretation of virial coefficients.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Gating and Intermolecular Interactions in Ligand-Protein Association: Coarse-Grained Modeling of HIV-1 Protease.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Modest protein-crowder attractive interactions can counteract enhancement of protein association by intermolecular excluded volume interactions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Free energy of sickle hemoglobin polymerization: a scaled-particle treatment for use with dextran as a crowding agent

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Distance of closest approach of two arbitrary hard ellipses in two dimensions.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

PIPER: an FFT-based protein docking program with pairwise potentials.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

General methods for free-volume theory.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

The Fourier-Green's function and the rapid evaluation of molecular potentials.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3811151

Influence of the shape of crowding particles on the structural transitions in a polymer

3 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24187527

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein Crowding Tunes Protein Stability

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24187527

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein docking using continuum electrostatics and geometric fit

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24187527

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT4005195

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json

29 February 2020

PubMed publication ID

24187527

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24187527%20AND%20SRC:MED&resulttype=core&format=json