Evidence map›Paper›PMID 41009484›Full record

ArticleInternational journal of molecular sciences2025

Accurate Protein Dynamic Conformational Ensembles: Combining AlphaFold, MD, and Amide

Dmitry Lesovoy, Konstantin Roshchin, Benedetta Maria Sala, Tatyana Sandalova, Adnane Achour, Tatiana Agback, Peter Agback, Vladislav Orekhov

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Full-Length Context Disrupts Folding of IgG-Binding Domains of Protein A.bioRxiv : the preprint server for biology · 2025
    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

8 authors.

Dmitry LesovoyShemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia.
Konstantin RoshchinShemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia.
Benedetta Maria SalaScience for Life Laboratory, Department of Medicine, Karolinska Institute, SE-171 65 Solna, Sweden.
Tatyana SandalovaScience for Life Laboratory, Department of Medicine, Karolinska Institute, SE-171 65 Solna, Sweden.
Adnane AchourScience for Life Laboratory, Department of Medicine, Karolinska Institute, SE-171 65 Solna, Sweden.ORCID 0000-0003-0432-710X
Tatiana AgbackDepartment of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 465, SE-405 30 Gothenburg, Sweden.ORCID 0000-0003-1325-6024
Peter AgbackDepartment of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden.ORCID 0000-0003-2226-0746
Vladislav OrekhovDepartment of Chemistry and Molecular Biology, University of Gothenburg, P.O. Box 465, SE-405 30 Gothenburg, Sweden.

Funding

Cancer och Allergi Fonden Cancer och Allergi Fonden 10399RSF RSF 24-13-00413Swedish Cancer Society Swedish Cancer Society 21 1605 Pj 01 HSwedish Foundation for Strategic Research Swedish Foundation for Strategic Research grant ITM17-0218Swedish Research Council Swedish Research Council № 2021-05061; 2018-02874; 2023-03485; 2024-06251
6 · The paper itself

Abstract

Conformational heterogeneity is essential for protein function, yet validating theoretical molecular dynamics (MD) ensembles remains a significant challenge. In this study, we present an approach that integrates free MD simulations, starting from an AlphaFold-generated structure, with refined experimental NMR-relaxation data to identify biologically relevant holistic time-resolved 4D conformational ensembles. Specifically, we select trajectory segments (RMSD plateaus) consistent with experimental observables. For the extracellular region of

Indexed as

Bacterial ProteinsMolecular Dynamics SimulationAmidesMagnetic Resonance SpectroscopyNitrogen IsotopesNuclear Magnetic Resonance, BiomolecularProtein ConformationStreptococcus pneumoniaeAmidesBacterial ProteinsNitrogen Isotopes15N cross-correlated relaxation4D dynamical conformation ensemblesback-calculated NMR parameterspulse program optimizationStreptococcus pneumoniae protein

Identifiers

PMID41009484
PMCPMC12469643

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.