Daniel J Rigden (Daniel Rigden)

Scopus Author ID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 48

Top Topics

Molecular Dynamics Simulations

Duchenne Muscular Dystrophy

Cardiovascular Risk Factors

Top Venues

Acta crystallographica. Section D, Structural biology

bioRxiv : the preprint server for biology

Journal of cell science

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

Publications

Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science 137 (2) (2024)
Modibo Diallo, Cécile Courdier, Elina Mercier, Angèle Sequeira, Alicia Defay-Stinat, Claudio Plaisant, Shahram Mesdaghi, Daniel J Rigden, Sophie Javerzat, Eulalie Lasseaux, Laetitia Bourgeade, Séverine Audebert-Bellanger, Hélène Dollfus, Smail Hadj Rabia, Fanny Morice-Picard, Manon Philibert, Mohamed Kole Sidibé, Vasily M Smirnov, Ousmane Sylla, Vincent Michaud, Benoit Arveiler
Functional Characterization of Splice Variants in the Diagnosis of Albinism. International journal of molecular sciences 25 (16) (2024)
Modibo Diallo, Cécile Courdier, Elina Mercier, Angèle Sequeira, Alicia Defay-Stinat, Claudio Plaisant, Shahram Mesdaghi, Daniel J Rigden, Sophie Javerzat, Eulalie Lasseaux, Laetitia Bourgeade, Séverine Audebert-Bellanger, Hélène Dollfus, Smail Hadj Rabia, Fanny Morice-Picard, Manon Philibert, Mohamed Kole Sidibé, Vasily M Smirnov, Ousmane Sylla, Vincent Michaud, Benoit Arveiler
Functional Characterization of Splice Variants in the Diagnosis of Albinism. International journal of molecular sciences 25 (16) (2024)
Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science 137 (2) (2024)
Shahram Mesdaghi, Rebecca Price, Ming Li, Raymond Q Migrino, Jillian Madine, Daniel J Rigden
Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models. bioRxiv : the preprint server for biology (2024)
Shahram Mesdaghi, Rebecca Price, Ming Li, Raymond Q Migrino, Jillian Madine, Daniel J Rigden
Investigating Medin Cleavage Accessibility in MfgE8: Conformational Insights Derived from Molecular Dynamics Simulations and AlphaFold2 Models. bioRxiv : the preprint server for biology (2024)
Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science 137 (2) (2024)
Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science 137 (2) (2024)
Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science 137 (2) (2024)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. Proteins (2023)
Andriy Kryshtafovych, Gaetano T Montelione, Daniel J Rigden, Shahram Mesdaghi, Ezgi Karaca, John Moult
Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. Proteins (2023)
Hannah L Glover, Marta Mendes, Joana Gomes-Neto, Emma V Rusilowicz-Jones, Daniel J Rigden, Gunnar Dittmar, Sylvie Urbé, Michael J Clague
Microtubule association of TRIM3 revealed by differential extraction proteomics. Journal of cell science (2023)
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)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Adam J Simpkin, Iracema Caballero, Stuart McNicholas, Kyle Stevenson, Elisabet Jiménez, Filomeno Sánchez Rodríguez, Maria Fando, Ville Uski, Charles Ballard, Grzegorz Chojnowski, Andrey A Lebedev, Eugene B Krissinel, Isabel Usón, Daniel J Rigden, Ronan M Keegan
Predicted models and CCP4. Acta crystallographica. Section D, Structural biology (2023)
Thomas Mulvaney, Rachael C Kretsch, Luc Elliott, Joseph George Beton, Andriy Kryshtafovych, Daniel J Rigden, Rachel J Hagey, Andriy Kryshtafovych
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. bioRxiv : the preprint server for biology (2023)
Rachel J Hagey, Rachael C Kretsch, Adam J Simpkin, Thomas Mulvaney, Phillip Pham, Ramya Rangan, Fan Bu, Ronan M Keegan, Andriy Kryshtafovych, Daniel J Rigden, Zhichiao Miao, Eric Westhof
Assessment of three-dimensional RNA structure prediction in CASP15. bioRxiv : the preprint server for biology (2023)
Andriy Kryshtafovych, Daniel J Rigden
To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units. Proteins (2023)
Thomas Mulvaney, Rachael C Kretsch, Luc Elliott, Joseph George Beton, Andriy Kryshtafovych, Daniel J Rigden, Rachel J Hagey, Andriy Kryshtafovych
CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Proteins 91 (12) (2023)
Adam J Simpkin, Shahram Mesdaghi, Filomeno Sánchez Rodríguez, Luc Elliott, David L Murphy, Andriy Kryshtafovych, Ronan M Keegan, Daniel J Rigden
Tertiary structure assessment at CASP15. Proteins (2023)
Filomeno Sánchez Rodríguez, Grzegorz Chojnowski, Ronan M Keegan, Daniel J Rigden
Using deep-learning predictions of inter-residue distances for model validation. Acta crystallographica. Section D, Structural biology 78 (Pt 12) (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)
Lucy C Ward, Hannah V McCue, Daniel J Rigden, Neil M Kershaw, Chloe Ashbrook, Harry Hatton, Ellie Goulding, James R Johnson, Andrew J Carnell
Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. Angewandte Chemie (International ed. in English) 61 (14) (2022)
Adam J Simpkin, Jens M H Thomas, Ronan M Keegan, Daniel J Rigden
MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more. Acta crystallographica. Section D, Structural biology 78 (Pt 5) (2022)
Elin Engdahl, Maarten D M van Schijndel, Dimitrios Voulgaris, Michela Di Criscio, Kerry A Ramsbottom, Daniel J Rigden, Anna Herland, Joëlle Rüegg
Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP). International journal of molecular sciences 22 (11) (2021)
Claudia Millán, Ronan M Keegan, Joana Pereira, Massimo D Sammito, Adam J Simpkin, Airlie J McCoy, Andrei N Lupas, Marcus D Hartmann, Daniel J Rigden, Randy J Read
Assessing the utility of CASP14 models for molecular replacement. Proteins 89 (12) (2021)
Jingxu Guo, Ronan M Keegan, Daniel J Rigden, Peter T Erskine, Steve P Wood, Sheng Li, Jonathan B Cooper
The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori. Acta crystallographica. Section F, Structural biology communications 77 (Pt 12) (2021)
Joana Pereira, Adam J Simpkin, Marcus D Hartmann, Daniel J Rigden, Ronan M Keegan, Andrei N Lupas
High-accuracy protein structure prediction in CASP14. Proteins 89 (12) (2021)
Olga V Moroz, Elena Blagova, Andrey A Lebedev, Filomeno Sánchez Rodríguez, Daniel J Rigden, Jeppe Wegener Tams, Reinhard Wilting, Jan Kjølhede Vester, Elena Longhin, Gustav Hammerich Hansen, Kristian Bertel Rømer Mørkeberg Krogh, Roland A Pache, Gideon J Davies, Keith S Wilson
Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions. Acta crystallographica. Section D, Structural biology 77 (Pt 12) (2021)
Grzegorz Chojnowski, Adam J Simpkin, Diego A Leonardo, Wolfram Seifert-Davila, Dan E Vivas-Ruiz, Ronan M Keegan, Daniel J Rigden
findMySequence : a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCrJ 9 (Pt 1) (2021)
Adam J Simpkin, Filomeno Sánchez Rodríguez, Shahram Mesdaghi, Andriy Kryshtafovych, Daniel J Rigden
Evaluation of model refinement in CASP14. Proteins 89 (12) (2021)
Adam J Simpkin, Martyn David Winn, Daniel J Rigden, Ronan M Keegan
Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM. Acta crystallographica. Section D, Structural biology 77 (Pt 11) (2021)
Filomeno Sánchez Rodríguez, Shahram Mesdaghi, Adam J Simpkin, J Javier Burgos-Mármol, David L Murphy, Ville Uski, Ronan M Keegan, Daniel J Rigden
ConPlot: web-based application for the visualization of protein contact maps integrated with other data. Bioinformatics (Oxford, England) 37 (17) (2021)
Jens M H Thomas, Ronan M Keegan, Daniel J Rigden, Owen Richard Davies
Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling. Acta crystallographica. Section D, Structural biology 76 (Pt 3) (2020)
Filomeno Sánchez Rodríguez, Adam J Simpkin, Owen Richard Davies, Ronan M Keegan, Daniel J Rigden
Helical ensembles outperform ideal helices in molecular replacement. Acta crystallographica. Section D, Structural biology 76 (Pt 10) (2020)
Aveline Hewetson, Nazmul H Khan, Matthew J Dominguez, Hoa Quynh Do, R E Kusko, Collin G Borcik, Daniel J Rigden, Ronan M Keegan, R Bryan Sutton, Michael P Latham, Benjamin J Wylie, Gail A Cornwall
Maturation of the functional mouse CRES amyloid from globular form. Proceedings of the National Academy of Sciences of the United States of America 117 (28) (2020)
Adam J Simpkin, Felix Simkovic, Jens M H Thomas, Martin Savko, Andrey Lebedev, Ville Uski, Charles C Ballard, Marcin Wojdyr, William Shepard, Daniel J Rigden, Ronan M Keegan
Using Phaser and ensembles to improve the performance of SIMBAD. Acta crystallographica. Section D, Structural biology 76 (Pt 1) (2020)
Adam J Simpkin, Jens M H Thomas, Felix Simkovic, Ronan M Keegan, Daniel J Rigden
Molecular replacement using structure predictions from databases. Acta crystallographica. Section D, Structural biology 75 (Pt 12) (2019)
Grace M Loxley, Jennifer Unsworth, Michael J Turton, Alexandra Jebb, Kathryn S Lilley, Deborah M Simpson, Daniel J Rigden, Jane L Hurst, Robert J Beynon
Glareosin: a novel sexually dimorphic urinary lipocalin in the bank vole, Myodes glareolus. Open biology 7 (9) (2018)
Ronan M Keegan, Stuart J McNicholas, Jens M H Thomas, Adam J Simpkin, Felix Simkovic, Ville Uski, Charles C Ballard, Martyn David Winn, Keith S Wilson, Daniel J Rigden
Recent developments in MrBUMP: better search-model preparation, graphical interaction with search models, and solution improvement and assessment. Acta crystallographica. Section D, Structural biology 74 (Pt 3) (2018)
Mara Kozic, Stephen J Fox, Jens M Thomas, Chandra S Verma, Daniel J Rigden
Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. Proteins 86 (5) (2018)
Daniel J Rigden, Jens M H Thomas, Felix Simkovic, Adam Simpkin, Martyn David Winn, Olga Mayans, Ronan M Keegan
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE. Acta crystallographica. Section D, Structural biology 74 (Pt 3) (2018)
Adam J Simpkin, Felix Simkovic, Jens M H Thomas, Martin Savko, Andrey Lebedev, Ville Uski, Charles Ballard, Marcin Wojdyr, Rui Wu, Ruslan Sanishvili, Yibin Xu, María Natalia Lisa, Alejandro Buschiazzo, William Shepard, Daniel J Rigden, Ronan M Keegan
SIMBAD: a sequence-independent molecular-replacement pipeline. Acta crystallographica. Section D, Structural biology 74 (Pt 7) (2018)
Jens M H Thomas, Felix Simkovic, Ronan Keegan, Olga Mayans, Chengxin Zhang, Yang Zhang, Daniel J Rigden
Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta crystallographica. Section D, Structural biology 73 (Pt 12) (2017)
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Applications of contact predictions to structural biology. IUCrJ 4 (Pt 3) (2017)
Adam J Simpkin, Daniel J Rigden
GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. BMC research notes 9 (2016)
Tiankun Zhou, Jennifer R Fleming, Barbara Franke, Julius Bogomolovas, Igor Barsukov, Daniel J Rigden, Siegfried Labeit, Olga Mayans
CARP interacts with titin at a unique helical N2A sequence and at the domain Ig81 to form a structured complex. FEBS letters 590 (18) (2016)