Evidence map›Paper›PMID 42630059›Full record

ReviewGlycobiology2026

Ten years of integrative carbohydrate structure validation with Privateer.

Lucy C Schofield, Jordan S Dialpuri, Haroldas Bagdonas, Lou Holland, Phuong Thao Pham, Shuai Wang, William Cook, Jon Agirre

Abstract readReview
In one paragraph

Review in Glycobiology, 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

8 authors.

Lucy C SchofieldYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
Jordan S DialpuriMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
Haroldas BagdonasYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
Lou HollandYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
Phuong Thao PhamYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
Shuai WangYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
William CookYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.
Jon AgirreYork Structural Biology Laboratory, Department of Chemistry, University of York, Wentworth way, York YO10 5DD, United Kingdom.ORCID 0000-0002-1086-0253

Funding

BBSRC BB/Y00888X/1Biotechnology and Biological Sciences Research Council BB/T0072221Chemistry Wild Fund PhD Studentship of the University of YorkRoyal Society RGF/R1/181006Royal Society URF\R\221006STFC/CCP4 4462290 (York) / S2 2024 012
6 · The paper itself

Abstract

Understanding glycoprotein structures is critical for understanding their biological roles, yet despite the moderate size of the glycans, determining the structure of these atomic models presents unique challenges. Originally designed to help mine the Protein Data Bank for monosaccharides and their context, the Privateer carbohydrate validation software has evolved to become ubiquitous in carbohydrate model building workflows. Privateer detects issues affecting sugar stereochemistry, regiochemistry, pyranoside and furanoside ring conformation, as well as overall glycan conformation and composition. Supporting both X-ray crystallography and cryo-electron microscopy data, Privateer can communicate with refinement software to help restrain sugar rings to their minimal-energy conformations. In this work, we reflect on a decade of Privateer, documenting its core processes and best practices to serve as the primary citation for the software.

Indexed as

CarbohydratesGlycoproteinsPolysaccharidesSoftwareCarbohydrate ConformationCryoelectron MicroscopyCrystallography, X-RayModels, MolecularCarbohydratesGlycoproteinsPolysaccharidescryo-EMcrystallographyglycansglycoproteinsvalidation

Identifiers

PMID42630059
PMCPMC7619613

What OpenQuestion holds

Textmetadata
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.