Evidence map›Paper›PMID 20886924›Full record

ArticleThe Journal of chemical physics2010

Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

J W Mullinax, W G Noid

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
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

8 citing papers in PubMed.

  1. Assignment of a Physical Energy Scale for the Dimensionless Interaction Energies within the PRIME20 Peptide Model.Chemphyschem : a European journal of chemical physics and physical chemistry · 2024
    Article
  2. Article
  3. Article
  4. Bottom-up Coarse-Graining: Principles and Perspectives.Journal of chemical theory and computation · 2022
    Review
  5. Article
  6. Article
  7. Review
  8. Recovering physical potentials from a model protein databank.Proceedings of the National Academy of Sciences of the United States of America · 2010
    Article
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

2 authors.

J W MullinaxDepartment of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
W G Noid

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Coarse-grained (CG) models provide a computationally efficient means for investigating phenomena that remain beyond the scope of atomically detailed models. Although CG models are often parametrized to reproduce the results of atomistic simulations, it is highly desirable to determine accurate CG models from experimental data. Recently, we have introduced a generalized Yvon-Born-Green (g-YBG) theory for directly (i.e., noniteratively) determining variationally optimized CG potentials from structural correlation functions. In principle, these correlation functions can be determined from experiment. In the present work, we introduce a reference state potential into the g-YBG framework. The reference state defines a fixed contribution to the CG potential. The remaining terms in the potential are then determined, such that the combined potential provides an optimal approximation to the many-body potential of mean force. By specifying a fixed contribution to the potential, the reference state significantly reduces the computational complexity and structural information necessary for determining the remaining potentials. We also validate the quantitative accuracy of the proposed method and numerically demonstrate that the reference state provides a convenient framework for transferring CG potentials from neat liquids to more complex systems. The resulting CG model provides a surprisingly accurate description of the two- and three-particle solvation structures of a hydrophobic solute in methanol. This work represents a significant step in developing the g-YBG theory as a useful computational framework for determining accurate CG models from limited experimental data.

Indexed as

Hydrophobic and Hydrophilic InteractionsModels, ChemicalWettabilityMarsileaceaeMethanolMethodsMolecular StructureSolubilitySolventsMethanolSolvents

Identifiers

PMID20886924
PMCPMC3188631

What OpenQuestion holds

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Registered trials

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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.