All Stories

  1. It’s Not Always Crystal Clear: In-Pocket Analysis for Understanding Binding Site Microenvironment Properties

    Article • September 2025, openRxiv

    Jon Agirre

  2. Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures

    Article • Protein Science, January 2025, Wiley

    Jon Agirre

  3. Welcoming Alejandro Buschiazzo, Dorothee Liebschner and Stephen Muench as Co-editors of Acta Crystallographica F – Structural Biology Communications

    Article • Acta Crystallographica Section F Structural Biology Communications, October 2024, International Union of Crystallography

    Jon Agirre

  4. Post-translational modifications in the Protein Data Bank

    Article • Acta Crystallographica Section D Structural Biology, August 2024, International Union of Crystallography

    Lucy Schofield, Jon Agirre

  5. NucleoFind: a deep-learning network for interpreting nucleic acid electron density

    Article • Nucleic Acids Research, August 2024, Oxford University Press (OUP)

    Jon Agirre

  6. The importance of international collaborations in science and structural biology

    Article • Acta Crystallographica Section F Structural Biology Communications, June 2024, International Union of Crystallography

    Jon Agirre

  7. Monitoring carbohydrate 3D structure quality with the Privateer database

    Article • Beilstein Journal of Organic Chemistry, April 2024, Beilstein Institut

    Jon Agirre

  8. Beyond publishing: introducing Interviews with authors

    Article • Acta Crystallographica Section F Structural Biology Communications, April 2024, International Union of Crystallography

    Jon Agirre

  9. Monitoring carbohydrate 3D structure quality with the Privateer database

    Article • January 2024, Beilstein Institut

    Jon Agirre

  10. Online Carbohydrate 3D Structure Validation with Privateer Web App

    Article • Acta Crystallographica Section F Structural Biology Communications, January 2024, International Union of Crystallography

    Jon Agirre

  11. Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif

    Article • Nature Communications, January 2024, Springer Science + Business Media

    Jon Agirre

  12. Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

    Article • Database, January 2024, Oxford University Press (OUP)

    Jon Agirre

  13. Using structural genomics depositions in undergraduate teaching of protein crystallography: everybody wins

    Article • Acta Crystallographica Section F Structural Biology Communications, October 2023, International Union of Crystallography

    Jon Agirre

  14. The CCP4 suite: integrative software for macromolecular crystallography

    Article • Acta Crystallographica Section D Structural Biology, May 2023, International Union of Crystallography

    Jon Agirre, Dr Gwyndaf Evans

  15. Analysis and validation of overall N-glycan conformation in Privateer

    Article • Acta Crystallographica Section D Structural Biology, May 2023, International Union of Crystallography

    Jon Agirre

  16. Model building and beyond

    Article • Acta Crystallographica Section D Structural Biology, October 2022, International Union of Crystallography

    Jon Agirre

  17. Whole-proteome structures shed new light on posttranslational modifications

    Article • PLoS Biology, May 2022, PLOS

    Jon Agirre

  18. Updated restraint dictionaries for carbohydrates in the pyranose form

    Article • Acta Crystallographica Section D Structural Biology, March 2022, International Union of Crystallography

    Jon Agirre

  19. The case for post-predictional modifications in the AlphaFold Protein Structure Database

    Article • Nature Structural & Molecular Biology, October 2021, Springer Science + Business Media

    Jon Agirre

  20. Towards consistency in geometry restraints for carbohydrates in the pyranose form: modern dictionary generators reviewed

    Article • Current Medicinal Chemistry, September 2021, Bentham Science Publishers

    Jon Agirre

  21. Iris: Interactive all‐in‐one graphical validation of 3D protein model iterations

    Article • Protein Science, October 2020, Wiley

    Jon Agirre

  22. Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

    Article • Beilstein Journal of Organic Chemistry, October 2020, Beilstein Institut

    Jon Agirre

  23. Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

    Article • July 2020, Beilstein Institut

    Jon Agirre

  24. The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PL39

    Article • Journal of Biological Chemistry, November 2019, Elsevier

    Jon Agirre

  25. Structural glycobiology in the age of electron cryo-microscopy

    Article • September 2019, Center for Open Science

    Jon Agirre

  26. The structure of the AliC GH13 α-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the α-amylase family

    Article • Acta Crystallographica Section D Structural Biology, January 2019, International Union of Crystallography

    Jon Agirre

  27. Carbohydrate structure hits the groove

    Article • Acta Crystallographica Section F Structural Biology Communications, August 2018, International Union of Crystallography

    Jon Agirre

  28. Macromolecular refinement by model morphing using non-atomic parameterizations

    Article • Acta Crystallographica Section D Structural Biology, February 2018, International Union of Crystallography

    Jon Agirre

  29. CCP4i2: the new graphical user interface to theCCP4 program suite

    Article • Acta Crystallographica Section D Structural Biology, February 2018, International Union of Crystallography

    Jon Agirre

  30. Automating tasks in protein structure determination with the clipper python module

    Article • Protein Science, November 2017, Wiley

    Jon Agirre, Tristan Croll

  31. Forty years of collaborative computational crystallography

    Article • Protein Science, October 2017, Wiley

    Jon Agirre

  32. Strategies for carbohydrate model building, refinement and validation

    Article • Acta Crystallographica Section D Structural Biology, February 2017, International Union of Crystallography

    Jon Agirre

  33. Glycoblocks: a schematic three-dimensional representation for glycans and their interactions

    Article • Acta Crystallographica Section D Structural Biology, September 2016, International Union of Crystallography

    Jon Agirre

  34. Privateer: software for the conformational validation of carbohydrate structures

    Article • Nature Structural & Molecular Biology, November 2015, Nature

    Professor Gideon J Davies, Jon Agirre

  35. Carbohydrate anomalies in the PDB

    Article • Nature Chemical Biology, April 2015, Nature

    Professor Gideon J Davies, Jon Agirre

  36. The Ever Changing Moods of Calmodulin: How Structural Plasticity Entails Transductional Adaptability

    Article • Journal of Molecular Biology, July 2014, Elsevier

    Jon Agirre, ALESSANDRO ALAIMO, Maurizio Taglialatela

  37. Molecular Techniques for Dicistrovirus Detection without RNA Extraction or Purification

    Article • BioMed Research International, January 2013, Hindawi Publishing Corporation

    Jon Agirre