Martini 3 as a Transferable Force Field for Lipopolysaccharide Parametrization.

Gvantsa Gutishvili, Diane L Lynch, James C Gumbart

Abstract read

In one paragraph

Article in The journal of physical chemistry. B, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Gvantsa GutishviliSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.

Diane L LynchSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.

James C GumbartSchool of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.ORCID 0000-0002-1510-7842

Funding

Elucidating the mechanisms of protein secretion across the outer membrane by bacterial autotransportersR01GM148586 · NIGMS · GEORGIA INSTITUTE OF TECHNOLOGY · PI James C. Gumbart · 2023 to 2026

$1.8M

NIGMS NIH HHS R01 GM148586

6 · The paper itself

Abstract

Lipopolysaccharides (LPS), as critical components of the outer membrane (OM) of Gram-negative bacteria, play essential roles in maintaining bacterial integrity and mediating environmental interactions. All-atom molecular dynamics (AA-MD) simulations provide detailed insights into LPS behavior at atomic resolution, but they remain computationally limited in accessing biologically relevant time scales. Coarse-grained (CG) models, such as Martini 3, offer a computationally efficient alternative while retaining sufficient accuracy for key biophysical properties. Although Martini 3 has been widely applied to proteins and phospholipids, only a few LPS models have been developed within this framework, limiting its utility for bacterial OM studies. To address this gap, we developed and validated CG parameters for LPS from multiple medically relevant pathogens, including

Indexed as

LipopolysaccharidesMolecular Dynamics SimulationEscherichia coliPseudomonas aeruginosaSalmonella entericaLipopolysaccharides

Identifiers

PMID41818446

DOI10.1021/acs.jpcb.6c00050

PMCPMC13034417

What Socratic holds

Textmetadata

LicenceCC BY

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 Socratic graph.