Jon Agirre

ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 42

Top Venues

Acta crystallographica. Section F, Structural biology communications

Acta crystallographica. Section D, Structural biology

Nature communications

Beilstein journal of organic chemistry

The University of York

University of the Basque Country (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

The University of York Oct 01 2017

United Kingdom

Royal Society University Research Fellow :: Chemistry

University of York Apr 10 2015 - Sep 30 2017

United Kingdom

PDRA in Structural Biology - method development :: Department of Chemistry

University of York Apr 10 2013 - Apr 09 2015

United Kingdom

PDRA in Structural Biology :: Department of Chemistry

Education History

University of the Basque Country Sep 01 2004 - May 19 2009

Spain

PHD :: Biochemistry

Publications

Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
Beyond publishing: introducing Interviews with authors. Acta crystallographica. Section F, Structural biology communications 80 (Pt 4) (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
Beyond publishing: introducing Interviews with authors. Acta crystallographica. Section F, Structural biology communications (2024)
Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Jordan S Dialpuri, Jon Agirre, Kathryn D Cowtan, Paul S Bond
NucleoFind: a deep-learning network for interpreting nucleic acid electron density. Nucleic acids research (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
Beyond publishing: introducing Interviews with authors. Acta crystallographica. Section F, Structural biology communications 80 (Pt 4) (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre
Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications 80 (Pt 2) (2024)
Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Noemi Arighi, Kristian B Axelsen, Evan E Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, Ten Feizi, Catherine Hayes, Callum M Ives, Hiren Jitendra Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frederique Lisacek, Yan Liu, Thomas Lütteke, Junfeng Ma, Adnan Malik, Maria Jesus Martin, Akul Y Mehta, Sriram Neelamegham, Kalpana Panneerselvam, René Ranzinger, Sylvie Ricard-Blum, Gaoussou Sanou, Vijay Shanker, Paul D Thomas, Michael Tiemeyer, James Urban, Randi Vita, Jeet Vora, Yasunori Yamamoto, Raja Mazumder
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database : the journal of biological databases and curation 2024 (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre
Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications (2024)
Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Noemi Arighi, Kristian B Axelsen, Evan E Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, Ten Feizi, Catherine Hayes, Callum M Ives, Hiren Jitendra Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frederique Lisacek, Yan Liu, Thomas Lütteke, Junfeng Ma, Adnan Malik, Maria Jesus Martin, Akul Y Mehta, Sriram Neelamegham, Kalpana Panneerselvam, René Ranzinger, Sylvie Ricard-Blum, Gaoussou Sanou, Vijay Shanker, Paul D Thomas, Michael Tiemeyer, James Urban, Randi Vita, Jeet Vora, Yasunori Yamamoto, Raja Mazumder
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database : the journal of biological databases and curation 2024 (2024)
Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
The importance of international collaborations in science and structural biology. Acta crystallographica. Section F, Structural biology communications 80 (Pt 6) (2024)
Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F Aoki-Kinoshita, Cecilia Noemi Arighi, Kristian B Axelsen, Evan E Bolton, Emily Bordeleau, Nathan J Edwards, Elisa Fadda, Ten Feizi, Catherine Hayes, Callum M Ives, Hiren Jitendra Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frederique Lisacek, Yan Liu, Thomas Lütteke, Junfeng Ma, Adnan Malik, Maria Jesus Martin, Akul Y Mehta, Sriram Neelamegham, Kalpana Panneerselvam, René Ranzinger, Sylvie Ricard-Blum, Gaoussou Sanou, Vijay Shanker, Paul D Thomas, Michael Tiemeyer, James Urban, Randi Vita, Jeet Vora, Yasunori Yamamoto, Raja Mazumder
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database : the journal of biological databases and curation 2024 (2024)
Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre
Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications 80 (Pt 2) (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Jon Agirre
Monitoring carbohydrate 3D structure quality with the Privateer database. Beilstein journal of organic chemistry 20 (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre
Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications 80 (Pt 2) (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
The importance of international collaborations in science and structural biology. Acta crystallographica. Section F, Structural biology communications 80 (Pt 6) (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Jon Agirre
Monitoring carbohydrate 3D structure quality with the Privateer database. Beilstein journal of organic chemistry 20 (2024)
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre
Online carbohydrate 3D structure validation with the Privateer web app. Acta crystallographica. Section F, Structural biology communications 80 (Pt 2) (2024)
Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Maria Cristina Nonato, Mark J van Raaij, Jon Agirre
Beyond publishing: introducing Interviews with authors. Acta crystallographica. Section F, Structural biology communications 80 (Pt 4) (2024)
Isabel Pérez-Jover, Kristy Rochon, Di Hu, Mukesh Mahajan, Pooja Madan Mohan, Isaac Santos-Pérez, Julene Ormaetxea Gisasola, Juan Manuel Martinez Galvez, Jon Agirre, Xin Qi, Jason A Mears, Anna V Shnyrova, Rajesh Ramachandran
Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nature communications 15 (1) (2024)
Lucy C Schofield, Jordan S Dialpuri, Garib N Murshudov, Jon Agirre
Post-translational modifications in the Protein Data Bank. Acta crystallographica. Section D, Structural biology (2024)
Jon Agirre, Mihaela Atanasova, Haroldas Bagdonas, Charles B Ballard, Arnaud Baslé, James Beilsten-Edmands, Rafael Junqueira Borges, David G Brown, J Javier Burgos-Mármol, John M Berrisford, Paul S Bond, Iracema Caballero, Lucrezia Catapano, Grzegorz Chojnowski, Atlanta G Cook, Kathryn D Cowtan, Tristan I Croll, Judit É Debreczeni, Nicholas E Devenish, Eleanor J Dodson, Tarik R Drevon, Paul Emsley, Gwyndaf Evans, Phil R Evans, Maria Fando, James Foadi, Luis Fuentes-Montero, Elspeth F Garman, Markus Gerstel, Richard J Gildea, Kaushik Hatti, Maarten L Hekkelman, Philipp Heuser, Soon Wen Hoh, Michael A Hough, Huw T Jenkins, Elisabet Jiménez, Robbie P Joosten, Ronan M Keegan, Nicholas H Keep, Eugene B Krissinel, Petr Kolenko, Oleg Kovalevskiy, Victor S Lamzin, David M Lawson, Andrey A Lebedev, Andrew G W Leslie, Bernhard Lohkamp, Fei Long, Martin Malý, Airlie J McCoy, Stuart J McNicholas, Ana Medina, Claudia Millán, James W Murray, Garib N Murshudov, Robert A Nicholls, Martin E M Noble, Robert D Oeffner, Navraj S Pannu, James M Parkhurst, Nicholas Pearce, Joana Pereira, Anastassis Perrakis, Harold R Powell, Randy J Read, Daniel J Rigden, William Rochira, Massimo D Sammito, Filomeno Sánchez Rodríguez, George M Sheldrick, Kathryn L Shelley, Felix Simkovic, Adam J Simpkin, Pavol Skubák, Egor Sobolev, Roberto A Steiner, Kyle Stevenson, Ivo Tews, Jens M H Thomas, Andrea Thorn, Josep Triviño Valls, Ville Uski, Isabel Usón, Alexei Vagin, Sameer Velankar, Melanie Vollmar, Helen Walden, David Geoffrey Waterman, Keith S Wilson, Martyn David Winn, Graeme Winter, Marcin Wojdyr, Keitaro Yamashita
The CCP4 suite: integrative software for macromolecular crystallography. Acta crystallographica. Section D, Structural biology 79 (Pt 6) (2023)
Jon Agirre
Using structural genomics depositions in undergraduate teaching of protein crystallography: everybody wins. Acta crystallographica. Section F, Structural biology communications 79 (Pt 10) (2023)
Jordan S Dialpuri, Haroldas Bagdonas, Mihaela Atanasova, Lucy C Schofield, Maarten L Hekkelman, Robbie P Joosten, Jon Agirre
Analysis and validation of overall N-glycan conformation in Privateer. Acta crystallographica. Section D, Structural biology (2023)
Jon Agirre, Robbie P Joosten, Alan Roseman
Model building and beyond. Acta crystallographica. Section D, Structural biology 78 (Pt 10) (2022)
Haroldas Bagdonas, Carl A Fogarty, Elisa Fadda, Jon Agirre
The case for post-predictional modifications in the AlphaFold Protein Structure Database. Nature structural & molecular biology 28 (11) (2022)
Robbie P Joosten, Jon Agirre
Whole-proteome structures shed new light on posttranslational modifications. PLoS biology 20 (5) (2022)
Eugene Krissinel, Andrey A Lebedev, Ville Uski, Charles B Ballard, Ronan M Keegan, Oleg Kovalevskiy, Robert A Nicholls, Navraj S Pannu, Pavol Skubák, John Berrisford, Maria Fando, Bernhard Lohkamp, Marcin Wojdyr, Adam J Simpkin, Jens M H Thomas, Christopher Oliver, Clemens Vonrhein, Grzegorz Chojnowski, Arnaud Basle, Andrew G Purkiss, Michail N Isupov, Stuart McNicholas, Edward Lowe, Josep Triviño, Kathryn D Cowtan, Jon Agirre, Daniel J Rigden, Isabel Uson, Victor S Lamzin, Ivo Tews, Gerard Bricogne, Andrew G W Leslie, David G Brown
CCP4 Cloud for structure determination and project management in macromolecular crystallography. Acta crystallographica. Section D, Structural biology 78 (Pt 9) (2022)
Mihaela Atanasova, Robert A Nicholls, Robbie P Joosten, Jon Agirre
Updated restraint dictionaries for carbohydrates in the pyranose form. Acta crystallographica. Section D, Structural biology 78 (Pt 4) (2022)
Pu Qian, Alastair T Gardiner, Ivana Šímová, Katerina Naydenova, Tristan I Croll, Philip J Jackson, Nupur, Miroslav Kloz, Petra Čubáková, Marek Kuzma, Yonghui Zeng, Pablo Castro-Hartmann, Bart van Knippenberg, Kenneth N Goldie, David Kaftan, Pavel Hrouzek, Jan Hájek, Jon Agirre, C Alistair Siebert, David Bína, Kasim Sader, Henning Stahlberg, Roman Sobotka, Christopher J Russo, Tomáš Polívka, Christopher Neil Hunter, Michal Koblížek
2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem. Science advances 8 (7) (2022)
Haroldas Bagdonas, Daniel Ungar, Jon Agirre
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer. Beilstein journal of organic chemistry 16 (2020)
William Rochira, Jon Agirre
Iris: Interactive all-in-one graphical validation of 3D protein model iterations. Protein science : a publication of the Protein Society 30 (1) (2020)
Jon Agirre, Olga V Moroz, Sebastian Meier, Jesper Brask, Astrid Munch, Tine Hoff, Carsten Andersen, Keith S Wilson, Gideon J Davies
The structure of the AliC GH13 α-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the α-amylase family. Acta crystallographica. Section D, Structural biology 75 (Pt 1) (2019)
Liz Potterton, Jon Agirre, Charles Ballard, Kathryn D Cowtan, Eleanor Dodson, Phil R Evans, Huw T Jenkins, Ronan Keegan, Eugene Krissinel, Kyle Stevenson, Andrey Lebedev, Stuart J McNicholas, Robert A Nicholls, Martin Noble, Navraj S Pannu, Christian Roth, George Sheldrick, Pavol Skubak, Johan P Turkenburg, Ville Uski, Frank von Delft, David Geoffrey Waterman, Keith S Wilson, Martyn David Winn, Marcin Wojdyr
CCP4i2: the new graphical user interface to the CCP4 program suite. Acta crystallographica. Section D, Structural biology 74 (Pt 2) (2018)
Kathryn D Cowtan, Jon Agirre
Macromolecular refinement by model morphing using non-atomic parameterizations. Acta crystallographica. Section D, Structural biology 74 (Pt 2) (2018)
Jon Agirre, Mark J van Raaij
Carbohydrate structure hits the groove. Acta crystallographica. Section F, Structural biology communications 74 (Pt 8) (2018)
Stuart McNicholas, Tristan Croll, Tom Burnley, Colin M Palmer, Soon Wen Hoh, Huw T Jenkins, Eleanor Dodson, Kathryn D Cowtan, Jon Agirre
Automating tasks in protein structure determination with the clipper python module. Protein science : a publication of the Protein Society 27 (1) (2017)
Jon Agirre, Eleanor Dodson
Forty years of collaborative computational crystallography. Protein science : a publication of the Protein Society 27 (1) (2017)
Jon Agirre, Javier Iglesias-Fernández, Carme Rovira, Gideon J Davies, Keith S Wilson, Kathryn D Cowtan
Privateer: software for the conformational validation of carbohydrate structures. Nature structural & molecular biology 22 (11) (2016)
Jon Agirre, Gideon J Davies, Keith Wilson, Kevin Cowtan
Carbohydrate anomalies in the PDB. Nature chemical biology 11 (5) (2015)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jon Agirre