Evidence map›Paper›PMID 35129974›Full record

ArticleJournal of chemical information and modeling2022

Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models.

Owen C Madin, Simon Boothroyd, Richard A Messerly, Josh Fass, John D Chodera, Michael R Shirts

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Uncertainty Quantification forChemical reviews · 2026
    Review
  3. Article
  4. 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

6 authors.

Owen C MadinDepartment of Chemical & Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.ORCID 0000-0002-6736-3442
Simon BoothroydBoothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London, Greater London, United Kingdom, WC2H 9JQ.ORCID 0000-0002-3456-1872
Richard A MesserlyTheoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.
Josh FassTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, New York 10065, United States.
John D ChoderaComputational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States.ORCID 0000-0003-0542-119X
Michael R ShirtsDepartment of Chemical & Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.ORCID 0000-0003-3249-1097

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
Open data-driven infrastructure for building biomolecular force fields for predictive biophysics and drug designR01GM132386 · NIGMS · UNIVERSITY OF COLORADO · PI SHIRTS, MICHAEL R · 2020 to 2023
$3.1M
NCI NIH HHS P30 CA008748NIGMS NIH HHS R01 GM132386
6 · The paper itself

Abstract

A high level of physical detail in a molecular model improves its ability to perform high accuracy simulations but can also significantly affect its complexity and computational cost. In some situations, it is worthwhile to add complexity to a model to capture properties of interest; in others, additional complexity is unnecessary and can make simulations computationally infeasible. In this work, we demonstrate the use of Bayesian inference for molecular model selection, using Monte Carlo sampling techniques accelerated with surrogate modeling to evaluate the Bayes factor evidence for different levels of complexity in the two-centered Lennard-Jones + quadrupole (2CLJQ) fluid model. Examining three nested levels of model complexity, we demonstrate that the use of variable quadrupole and bond length parameters in this model framework is justified only for some chemistries. Through this process, we also get detailed information about the distributions and correlation of parameter values, enabling improved parametrization and parameter analysis. We also show how the choice of parameter priors, which encode previous model knowledge, can have substantial effects on the selection of models, penalizing careless introduction of additional complexity. We detail the computational techniques used in this analysis, providing a roadmap for future applications of molecular model selection via Bayesian inference and surrogate modeling.

Indexed as

Bayes TheoremComputer SimulationMonte Carlo Method

Identifiers

PMID35129974
PMCPMC9217127

What OpenQuestion holds

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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.