Implementation of Replica-Averaged Restraints from Nuclear Magnetic Resonance Measurement with UNRES Coarse Grained Model of Polypeptide Chains.

Leonid Shirkov, Cezary Czaplewski, Adam Liwo

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.

Leonid ShirkovFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0003-4351-5066

Cezary CzaplewskiFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0002-0294-3403

Adam LiwoFaculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Wita Stwosza 63, 80-308 Gdańsk, Poland.ORCID 0000-0001-6942-2226

Funding

National Science Centre UMO- 544 2021/40/Q/ST4/00035

6 · The paper itself

Abstract

We report the implementation of replica-averaged molecular dynamics in the UNRES coarse-grained model of polypeptide chains, with application to the restraints determined by nuclear magnetic resonance. The analytical ESCASA algorithm is used to estimate interproton distances from coarse-grained geometry. With synthetic restraints derived from two selected conformations of the L129-L153 loop of the Slr1183 protein from

Indexed as

Bacterial ProteinsIntrinsically Disordered ProteinsNuclear Magnetic Resonance, BiomolecularPeptidesAlgorithmsMagnetic Resonance SpectroscopyMolecular Dynamics SimulationProtein ConformationSynechocystisBacterial ProteinsIntrinsically Disordered ProteinsPeptidesdata-assisted modelingnuclear magnetic resonancereplica-averaged restraintsUNRES coarse-grained model

Identifiers

PMID41302413

DOI10.3390/molecules30224354

PMCPMC12654794

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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.