Rigden, Daniel J.

Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation

Polson, H. E. J., de Lartigue, J., Rigden, D. J., Reedijk, M., Urbé, S., Clague, M. J., & Tooze, S. A. (2010) · Autophagy

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High‐accuracy protein structure prediction in CASP14

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Protein Structure and DynamicsEnzyme Structure and Function

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Assessment of three‐dimensional RNA structure prediction in CASP15

Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., Bu, F., Keegan, R. M., Topf, M., Rigden, D. J., et al. (2023) · Proteins: Structure, Function, and Bioinformatics

RNA and protein synthesis mechanismsProtein Structure and Dynamics

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Prediction of antimicrobial peptides based on the adaptive neuro‐fuzzy inference system application

Fernandes, F. C., Rigden, D. J., & Franco, O. L. (2012) · Peptide Science

Antimicrobial Peptides and ActivitiesComputational Drug Discovery Methods

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Assessing the utility of CASP14 models for molecular replacement

Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics

Enzyme Structure and FunctionProtein Structure and Dynamics

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The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis

Nunes, Q. M., Su, D., Brownridge, P. J., Simpson, D. M., Sun, C., Li, Y., Bui, T. P., Zhang, X., Huang, W., Rigden, D. J., et al. (2018) · PLoS ONE

Pancreatitis Pathology and TreatmentPancreatic and Hepatic Oncology Research

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The heparin-binding proteome in normal pancreas and murine experimental acute pancreatitis

Nunes, Q. M., Su, D., Brownridge, P. J., Simpson, D. M., Sun, C., Li, Y., Bui, T. P., Zhang, X., Huang, W., Rigden, D. J., et al. (2019) · PLOS ONE

Pancreatitis Pathology and TreatmentPancreatic and Hepatic Oncology Research

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Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15

Kryshtafovych, A., Montelione, G. T., Rigden, D. J., Mesdaghi, S., Karaca, E., & Moult, J. (2023) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

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Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15

Kryshtafovych, A., Montelione, G., Rigden, D., Mesdaghi, S., Karaca, E., & Moult, J. (2023) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

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Evaluation of model refinement in CASP14

Simpkin, A. J., Sánchez Rodríguez, F., Mesdaghi, S., Kryshtafovych, A., & Rigden, D. J. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

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AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins

Pratt, O. S., Elliott, L. G., Haon, M., Mesdaghi, S., Price, R. M., Simpkin, A. J., & Rigden, D. J. (2024) · Computational and Structural Biotechnology Journal

Protein Structure and DynamicsEnzyme Structure and Function

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AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins

Pratt, O. S., Elliott, L. G., Haon, M., Mesdaghi, S., Price, R. M., Simpkin, A. J., & Rigden, D. J. (2025) · Computational and Structural Biotechnology Journal

Protein Structure and DynamicsEnzyme Structure and Function

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MrParse : finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more

Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022) · Acta Crystallographica Section D Structural Biology

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Structural insights into pink-eyed dilution protein (Oca2)

Mesdaghi, S., Murphy, D. L., Simpkin, A. J., & Rigden, D. J. (2023) · Bioscience Reports

Protein Structure and Dynamicsmelanin and skin pigmentation

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ABCFold: easier running and comparison of AlphaFold 3, Boltz-1, and Chai-1

Elliott, L. G., Simpkin, A. J., & Rigden, D. J. (2024) · Bioinformatics Advances

Protein Structure and DynamicsMachine Learning in Bioinformatics

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ABCFold: easier running and comparison of AlphaFold 3, Boltz-1 and Chai-1

Elliott, L. G., Simpkin, A. J., & Rigden, D. J. (2025) · Bioinformatics Advances

Protein Structure and DynamicsMachine Learning in Bioinformatics

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Using deep-learning predictions of inter-residue distances for model validation

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Protein Structure and DynamicsEnzyme Structure and Function

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The promise of AlphaFold for gene structure annotation

Davison, H. R., Böhme, U., Mesdaghi, S., Wilkinson, P. A., Roos, D. S., Jones, A. R., & Rigden, D. J. (2026) · Nucleic Acids Research

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