A Hybrid UA-CG Force Field for Aggregation Simulation of Amyloidogenic Peptide via Liquid-like Intermediates.

Abstract read

In one paragraph

Article in Molecules (Basel, Switzerland), 2025. 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.

Hang ZhengSchool of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.ORCID 0000-0002-2825-0576

Shu LiCentre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China.ORCID 0000-0002-4434-6172

Wei HanDepartment of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong 999077, China.ORCID 0000-0003-0759-1766

Funding

National Natural Science Foundation of China 21977011

6 · The paper itself

Abstract

Elucidating amyloid formation inside biomolecular condensates requires models that resolve (i) local, chemistry specific contacts controlling β registry and (ii) mesoscale phase behavior and cluster coalescence on microsecond timescales-capabilities beyond single resolution models. We present a hybrid united atom/coarse grained (UA-CG) force field coupling a PACE UA peptide model with the MARTINI CG framework. Cross resolution nonbonded parameters are first optimized against all atom side chain potentials of mean force to balance the relative strength between different types of interactions and then refined through universal parameter scaling by matching radius of gyration distributions for specific systems using. We applied this approach to simulate a recently reported model system comprising the LVFFAR

Indexed as

AmyloidAmyloidogenic ProteinsMolecular Dynamics SimulationPeptidesProtein AggregatesHumansAmyloidAmyloidogenic ProteinsPeptidesProtein Aggregatesamyloidogenesisbiomolecular condensateshybrid resolution simulationliquid–liquid phase separationreaction limited coalescence

Identifiers

PMID41097365

DOI10.3390/molecules30193946

PMCPMC12526129

What OpenQuestion 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 OpenQuestion graph.