Evidence map›Paper›PMID 42080355›Full record

ArticleJournal of chemical information and modeling2026

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Krzysztof K Bojarski, Patryk A Wesołowski, Diksha Dewan, Łukasz J Dziadek, Vilmos Neuman, Bernard R Brooks, Jacek Czub, Martin Zacharias, Adam K Sieradzan, David J Wales

Abstract readComparative Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical information and modeling, 2026. 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. Review
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

10 authors.

Krzysztof K BojarskiDepartment of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-308, Poland.ORCID 0000-0002-2066-1522
Patryk A WesołowskiYusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.ORCID 0000-0002-7751-980X
Diksha DewanYusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.ORCID 0000-0003-4333-0889
Łukasz J DziadekDepartment of Theoretical Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk 80-952, Poland.
Vilmos NeumanDepartment of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
Bernard R BrooksLaboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.
Jacek CzubDepartment of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk 80-308, Poland.ORCID 0000-0003-3639-6935
Martin ZachariasCenter for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching 85748, Germany.ORCID 0000-0001-5163-2663
Adam K SieradzanDepartment of Theoretical Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk 80-952, Poland.ORCID 0000-0002-2426-3644
David J WalesYusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.ORCID 0000-0002-3555-6645

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Glycosaminoglycans (GAGs) are long, anionic polysaccharides abundant in the extracellular matrix and lysosomes, where their electrostatic interactions with proteins are essential for biological function. Computational studies of GAG-containing systems remain challenging due to their significant charge density and conformational flexibility. Here we benchmark two widely used force-fields, ff14SB/GLYCAM06j-1 and CHARMM36m, for three experimentally characterized protein-GAG complexes. Both force fields reproduce the key structural features of protein-GAG interactions, while GAG dynamics depend on protein charge, with CHARMM36m favoring broader surface exploration for highly positively charged proteins and AMBER enhancing mobility for less charged systems. Although protein flexibility is similarly described, ff14SB/GLYCAM06j-1 samples a broader GAG conformational space, and dissociation free energy profiles diverge for highly anionic GAGs, but remain comparable for moderately sulfated systems. In addition, we performed molecular dynamics simulations for all systems using the ff14SB/GLYCAM06j-1, CHARMM36m, and ff19SB/GLYCAM06j-1 force fields in a 15 Å solvent box. Structural and energetic analyses revealed no significant impact of the solvent box size on the examined descriptors. These results establish practical benchmarks for accurate atomistic simulations of GAG-protein assemblies and will inform future developments in biomolecular force fields.

Indexed as

GlycosaminoglycansMolecular Dynamics SimulationProteinsProtein BindingProtein ConformationThermodynamicsGlycosaminoglycansProteins

Identifiers

PMID42080355
PMCPMC13213835

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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.