Evidence map›Paper›PMID 40108759›Full record

ArticleJournal of chemical theory and computation2025

Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization.

Yongxian Wu, Qiang Zhu, Zhen Huang, Piotr Cieplak, Yong Duan, Ray Luo

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical theory and computation, 2025. 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
–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

1 citing paper in PubMed.

  1. 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.

Yongxian WuDepartments of Chemical and Biomolecular Engineering, Molecular Biology and Biochemistry, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0000-0003-1497-2444
Qiang ZhuDepartments of Chemical and Biomolecular Engineering, Molecular Biology and Biochemistry, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0000-0002-5612-0728
Zhen HuangDepartments of Chemical and Biomolecular Engineering, Molecular Biology and Biochemistry, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0009-0003-4478-8477
Piotr CieplakSBP Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, United States.ORCID 0000-0003-0700-5691
Yong DuanUC Davis Genome Center and Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.ORCID 0000-0003-3793-5099
Ray LuoDepartments of Chemical and Biomolecular Engineering, Molecular Biology and Biochemistry, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California 92697, United States.ORCID 0000-0002-6346-8271

Funding

AMBER force field consortium: a coherent biomolecular simulation platformR01GM079383 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI CIEPLAK, PIOTR, DUAN, YONG · 2007 to 2017
$4.7M
Multi-scaled Modeling of Electrostatic and Polarization Effects in BiomoleculesR35GM130367 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI RAY LUO · 2019 to 2026
$3.0M
NIGMS NIH HHS R01 GM079383NIGMS NIH HHS R35 GM130367
6 · The paper itself

Abstract

The critical importance of water in sustaining life highlights the need for accurate water models in computer simulations, aiming to mimic biochemical processes experimentally. The polarizable Gaussian multipole (pGM) model, recently introduced for biomolecular simulations, improves the handling of complex biomolecular interactions. As an integral part of our initial exploration, we examined a minimalist fixed geometry three-center pGM water model using

Identifiers

PMID40108759
PMCPMC12665499

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.