Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.

R B Pandey, D J Jacobs, B L Farmer

Abstract read

In one paragraph

Article in The Journal of chemical physics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

0.7field-weighted citation impact, top 31% of its field

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 8 citations in OpenAlex.

Protein Function Analysis through Machine Learning.Biomolecules · 2022
Review

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors at 3 institutions in 1 country.

R B PandeyDepartment of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA.ORCID 0000000342338897

D J JacobsDepartment of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina 28223, USA.

B L FarmerMaterials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA and Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.

North Carolina State University · USUniversity of North Carolina at Charlotte · USUniversity of Southern Mississippi · US

Funding

Wellcome Trust

6 · The paper itself

Abstract

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (R

Indexed as

Monte Carlo MethodBinding SitesProtein ConformationProtein SProtein S

Identifiers

PMID28527439

DOI10.1063/1.4983222

PMCPMC5438306

OpenAlexW2616645895

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.