Professor Dan Rigden BA, PhD
Professor of Protein Bioinformatics Biochemistry, Cell and Systems Biology
- +44 (0)151 795 4467
- Work email Drigden@liverpool.ac.uk
- About
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Publications
Selected Publications
- Applications of contact predictions to structural biology (Journal article - 2017)
- The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection (Journal article - 2022)
- Assessing the utility of CASP14 models for molecular replacement (Journal article - 2021)
- Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications (Journal article - 2021)
- High-accuracy protein structure prediction in CASP14 (Journal article - 2021)
- Prophages encode phage-defense systems with cognate self-immunity (Journal article - 2021)
- In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. (Journal article - 2021)
- Using Phaser and ensembles to improve the performance of SIMBAD (Journal article - 2020)
- findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM (Journal article - 2022)
- Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM (Journal article - 2021)
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2024
m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. (Journal article)
Ye, H., Li, T., Rigden, D. J., & Wei, Z. (2024). m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq.. Nucleic acids research, gkae280. doi:10.1093/nar/gkae280The 2024 Nucleic Acids Research database issue and the online molecular biology database collection. (Journal article)
Rigden, D. J., & Fernández, X. M. (2024). The 2024 Nucleic Acids Research database issue and the online molecular biology database collection.. Nucleic acids research, 52(D1), D1-D9. doi:10.1093/nar/gkad1173KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival. (Journal article)
Saleh, H., Liloglou, T., Rigden, D. J., Parsons, J. L., & Grundy, G. J. (2024). KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival.. Journal of molecular biology, 436(4), 168434. doi:10.1016/j.jmb.2023.1684342023
Microtubule association of TRIM3 revealed by differential extraction proteomics. (Journal article)
Glover, H. L., Mendes, M., Gomes-Neto, J., Rusilowicz-Jones, E. V., Rigden, D. J., Dittmar, G., . . . Clague, M. J. (2023). Microtubule association of TRIM3 revealed by differential extraction proteomics.. Journal of cell science, jcs.261522. doi:10.1242/jcs.261522Deep Learning-based structural and functional annotation of Pandoravirus hypothetical proteins (Preprint)
Assessment of three-dimensional RNA structure prediction in CASP15. (Journal article)
Das, R., Kretsch, R. C., Simpkin, A. J., Mulvaney, T., Pham, P., Rangan, R., . . . Westhof, E. (2023). Assessment of three-dimensional RNA structure prediction in CASP15.. Proteins, 91(12), 1747-1770. doi:10.1002/prot.26602Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15. (Journal article)
Kryshtafovych, A., Montelione, G. T., Rigden, D. J., Mesdaghi, S., Karaca, E., & Moult, J. (2023). Breaking the conformational ensemble barrier: Ensemble structure modeling challenges in CASP15.. Proteins, 91(12), 1903-1911. doi:10.1002/prot.26584CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. (Journal article)
Mulvaney, T., Kretsch, R. C., Elliott, L., Beton, J. G., Kryshtafovych, A., Rigden, D. J., . . . Topf, M. (2023). CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps.. Proteins, 91(12), 1935-1951. doi:10.1002/prot.26644Tertiary structure assessment at CASP15 (Journal article)
Simpkin, A. J., Mesdaghi, S., Rodriguez, F. S., Elliott, L., Murphy, D. L., Kryshtafovych, A., . . . Rigden, D. J. (2023). Tertiary structure assessment at CASP15. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. doi:10.1002/prot.26593m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome (Journal article)
Wang, X., Zhang, Y., Chen, K., Liang, Z., Ma, J., Xia, R., . . . Song, B. (2023). m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m<SUP>7</SUP>G) epitranscriptome. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkad789Predicted models and <i>CCP</i>4 (Journal article)
Simpkin, A. J., Caballero, I., McNicholas, S., Stevenson, K., Jimenez, E., Rodriguez, F. S., . . . Keegan, R. M. (2023). Predicted models and <i>CCP</i>4. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79, 806-819. doi:10.1107/S2059798323006289Engineering a Carboxyl Methyltransferase for the Formation of a Furan-Based Bioplastic Precursor (Journal article)
Ward, L. C., Goulding, E., Rigden, D. J., Allan, F. E., Pellis, A., Hatton, H., . . . Carnell, A. J. (2023). Engineering a Carboxyl Methyltransferase for the Formation of a Furan-Based Bioplastic Precursor. CHEMSUSCHEM. doi:10.1002/cssc.202300516m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species (Journal article)
Liang, Z., Ye, H., Ma, J., Wei, Z., Wang, Y., Zhang, Y., . . . Chen, K. (2023). m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species. NUCLEIC ACIDS RESEARCH. doi:10.1093/nar/gkad691CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. (Preprint)
Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space (Journal article)
Mesdaghi, S., Price, R. M., Madine, J., & Rigden, D. J. (2023). Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space. Journal of Structural Biology, 108010. doi:10.1016/j.jsb.2023.108010m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues. (Journal article)
Song, B., Huang, D., Zhang, Y., Wei, Z., Su, J., Pedro de Magalhães, J., . . . Chen, K. (2023). m6A-TSHub: Unveiling the Context-specific m<sup>6</sup>A Methylation and m<sup>6</sup>A-affecting Mutations in 23 Human Tissues.. Genomics, proteomics & bioinformatics, 21(4), 678-694. doi:10.1016/j.gpb.2022.09.001Structural Insights into Pink-eyed Dilution Protein (Oca2). (Journal article)
Mesdaghi, S., Murphy, D. L., Simpkin, A. J., & Rigden, D. J. (2023). Structural Insights into Pink-eyed Dilution Protein (Oca2).. Bioscience reports, BSR20230060. doi:10.1042/bsr20230060CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (Preprint)
The <i>CCP4</i> suite: integrative software for macromolecular crystallography (Journal article)
Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Basle, A., Beilsten-Edmands, J., . . . Yamashita, K. (2023). The <i>CCP4</i> suite: integrative software for macromolecular crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 79, 449-461. doi:10.1107/S2059798323003595To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units (Journal article)
Kryshtafovych, A., & Rigden, D. J. (2023). To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. doi:10.1002/prot.26533Tertiary structure assessment at CASP15 (Preprint)
An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha. (Journal article)
Dusi, D. M. A., Alves, E. R., Cabral, G. B., Mello, L. V., Rigden, D. J., Silveira, É. D., . . . Carneiro, V. T. C. (2023). An exonuclease V homologue is expressed predominantly during early megasporogenesis in apomictic Brachiaria brizantha.. Planta, 258(1), 5. doi:10.1007/s00425-023-04162-8To split or not to split: CASP15 targets and their processing into tertiary structure evaluation units (Preprint)
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication (Journal article)
Song, B., Wang, X., Liang, Z., Ma, J., Huang, D., Wang, Y., . . . Wei, Z. (2023). RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. NUCLEIC ACIDS RESEARCH, 51(D1), D1388-D1396. doi:10.1093/nar/gkac750The 2023 <i>Nucleic Acids</i> <i>Research</i> Database Issue and the online molecular biology database collection (Journal article)
Rigden, D. J., & Fernandez, X. M. (2023). The 2023 <i>Nucleic Acids</i> <i>Research</i> Database Issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 51(D1), D1-D8. doi:10.1093/nar/gkac1186DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. (Journal article)
Zhang, Y., Jiang, J., Ma, J., Wei, Z., Wang, Y., Song, B., . . . Chen, K. (2023). DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.. Nucleic Acids Res., 51, 106-116.2022
Structural Insights into Pink-eyed Dilution Protein (Oca2) (Preprint)
Using deep-learning predictions of inter-residue distances for model validation (Journal article)
Rodriguez, F. S., Chojnowski, G., Keegan, R. M., & Rigden, D. J. (2022). Using deep-learning predictions of inter-residue distances for model validation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 1412-1427. doi:10.1107/S2059798322010415DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. (Journal article)
Zhang, Y., Jiang, J., Ma, J., Wei, Z., Wang, Y., Song, B., . . . Chen, K. (2022). DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.. Nucleic acids research, gkac1061. doi:10.1093/nar/gkac1061Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation (Journal article)
Huang, D., Chen, K., Song, B., Wei, Z., Su, J., Coenen, F., . . . Meng, J. (2022). Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. NUCLEIC ACIDS RESEARCH, 50(18), 10290-10310. doi:10.1093/nar/gkac830<i>CCP</i>4 Cloud for structure determination and project management in macromolecular crystallograpny (Journal article)
Krissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O., . . . Brown, D. G. (2022). <i>CCP</i>4 Cloud for structure determination and project management in macromolecular crystallograpny. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 1079-1089. doi:10.1107/S2059798322007987Using deep learning predictions of inter-residue distances for model validation (Preprint)
<i>Slice'N'Dice</i>: maximising predicted models for structural biologists (Journal article)
Simpkin, A. J., Elliot, L. G., Rigden, D. J., & Keegan, R. M. (2022). <i>Slice'N'Dice</i>: maximising predicted models for structural biologists. Acta Crystallographica Section A Foundations and Advances, 78(a2), e24. doi:10.1107/s2053273322096474Evolutionary covariance to assess the biological relevance of putative homo-oligomeric interfaces (Conference Paper)
Burgos-Marmol, J. J., Keegan, R. M., Krissinel, E., & Rigden, D. J. (2022). Evolutionary covariance to assess the biological relevance of putative homo-oligomeric interfaces. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 78 (pp. E434). Retrieved from https://www.webofscience.com/PDB-wide model validation using deep learning based predictions of distances and contacts (Journal article)
Sanchez Rodriguez, F., Chojnowski, G., Keegan, R., & Rigden, D. (2022). PDB-wide model validation using deep learning based predictions of distances and contacts. Acta Crystallographica Section A Foundations and Advances, 78(a2), e79. doi:10.1107/s2053273322095997Slice'N'Dice: maximising predicted models for structural biologists (Conference Paper)
Simpkin, A. J., Elliot, L. G., Rigden, D. J., & Keegan, R. M. (2022). Slice'N'Dice: maximising predicted models for structural biologists. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 78 (pp. E24). doi:10.1107/S2053273322096462Slice’N’Dice: Maximising the value of predicted models for structural biologists (Preprint)
WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction (Journal article)
Liu, L., Song, B., Chen, K., Zhang, Y., de Magalhaes, J. P., Rigden, D. J., . . . Wei, Z. (2022). WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. METHODS, 203, 378-382. doi:10.1016/j.ymeth.2021.07.003<i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more (Journal article)
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2022). <i>MrParse:</i> finding homologues in the PDB and the EBI AlphaFold database tor molecular replacement and more. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 78, 553-559. doi:10.1107/S2059798322003576Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis (Journal article)
Ward, L. C., McCue, H. V., Rigden, D. J., Kershaw, N. M., Ashbrook, C., Hatton, H., . . . Carnell, A. J. (2022). Carboxyl Methyltransferase Catalysed Formation of Mono- and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 61(14). doi:10.1002/anie.202117324Carboxyl Methyltransferase Catalysed Formation of Mono‐ and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis (Journal article)
Ward, L. C., McCue, H. V., Rigden, D. J., Kershaw, N. M., Ashbrook, C., Hatton, H., . . . Carnell, A. J. (2022). Carboxyl Methyltransferase Catalysed Formation of Mono‐ and Dimethyl Esters under Aqueous Conditions: Application in Cascade Biocatalysis. Angewandte Chemie, 134(14). doi:10.1002/ange.202117324Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs (Journal article)
Bengtsson, R. J., Simpkin, A. J., Pulford, C. V., Low, R., Rasko, D. A., Rigden, D. J., . . . Baker, K. S. (2022). Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. NATURE MICROBIOLOGY. doi:10.1038/s41564-021-01054-zm6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues (Preprint)
The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection (Journal article)
Rigden, D. J., & Fernandez, X. M. (2022). The 2022 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 50(D1), D1-D10. doi:10.1093/nar/gkab1195m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. (Journal article)
Ma, J., Song, B., Wei, Z., Huang, D., Zhang, Y., Su, J., . . . Chen, K. (2022). m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.. Nucleic acids research, 50(D1), D196-D203. doi:10.1093/nar/gkab1075findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM (Journal article)
Chojnowski, G., Simpkin, A. J., Leonardo, D. A., Seifert-Davila, W., Vivas-Ruiz, D. E., Keegan, R. M., & Rigden, D. J. (2022). findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. IUCrJ, 9(1), 86-97. doi:10.1107/s20522525210110882021
Assessing the utility of CASP14 models for molecular replacement (Journal article)
Millan, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., . . . Read, R. J. (2021). Assessing the utility of CASP14 models for molecular replacement. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1752-1769. doi:10.1002/prot.26214Evaluation of model refinement in CASP14 (Journal article)
Simpkin, A. J., Sanchez Rodriguez, F., Mesdaghi, S., Kryshtafovych, A., & Rigden, D. J. (2021). Evaluation of model refinement in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1852-1869. doi:10.1002/prot.26185High-accuracy protein structure prediction in CASP14 (Journal article)
Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021). High-accuracy protein structure prediction in CASP14. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 89(12), 1687-1699. doi:10.1002/prot.26171Multitasking in the gut: the X-ray structure of the multidomain BbgIII from Bifidobacterium bifidum offers possible explanations for its alternative functions (Journal article)
Moroz, O. V., Blagova, E., Lebedev, A. A., Rodriguez, F. S., Rigden, D. J., Tams, J. W., . . . Wilson, K. S. (2021). 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, 1564-1578. doi:10.1107/S2059798321010949The X-ray structure of juvenile hormone diol kinase from the silkworm <i>Bombyx mori</i> (Journal article)
Guo, J., Keegan, R. M., Rigden, D. J., Erskine, P. T., Wood, S. P., Li, S., & Cooper, J. B. (2021). The X-ray structure of juvenile hormone diol kinase from the silkworm <i>Bombyx mori</i>. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 77, 465-472. doi:10.1107/S2053230X21012012Prophages encode phage-defense systems with cognate self-immunity (Journal article)
Owen, S. V., Wenner, N., Dulberger, C. L., Rodwell, E. V., Bowers-Barnard, A., Quinones-Olvera, N., . . . Hinton, J. C. D. (2021). Prophages encode phage-defense systems with cognate self-immunity. CELL HOST & MICROBE, 29(11), 1620-+. doi:10.1016/j.chom.2021.09.002ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome (Journal article)
Song, B., Chen, K., Tang, Y., Wei, Z., Su, J., de Magalhaes, J. P., . . . Meng, J. (2021). ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. BRIEFINGS IN BIOINFORMATICS, 22(6). doi:10.1093/bib/bbab088Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM (Journal article)
Simpkin, A. J., Winn, M. D., Rigden, D. J., & Keegan, R. M. (2021). Redeployment of automated MrBUMP searchmodel identification for map fitting in cryo-EM. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 77, 1378-1385. doi:10.1107/S2059798321009165MrParse: Finding homologues in the PDB and the EBI AlphaFold database for Molecular Replacement and more (Preprint)
Applications of residue contact predictions in structural biology (Conference Paper)
Rodriguez, F. S., Keegan, R. M., Vollmar, M., Evans, G., & Rigden, D. J. (2021). Applications of residue contact predictions in structural biology. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C48). Retrieved from https://www.webofscience.com/Exploiting new generation ab initio and homology models from databases for MR (Conference Paper)
Simpkin, A. J., Thomas, J. M. H., Keegan, R. M., & Rigden, D. J. (2021). Exploiting new generation ab initio and homology models from databases for MR. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C688). Retrieved from https://www.webofscience.com/PISACov: Expanding jsPISA with evolutionary covariance data to better determine protein quaternary state from a crystal structure (Conference Paper)
Burgos-Marmol, J. J., Keegan, R. M., Krissinel, E., & Rigden, D. J. (2021). PISACov: Expanding jsPISA with evolutionary covariance data to better determine protein quaternary state from a crystal structure. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES Vol. 77 (pp. C693). Retrieved from https://www.webofscience.com/Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications (Journal article)
Song, Z., Huang, D., Song, B., Chen, K., Song, Y., Liu, G., . . . Meng, J. (2021). Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-24313-3Assessing the utility of CASP14 models for molecular replacement (Preprint)
Assessing the utility of CASP14 models for molecular replacement (Preprint)
Informing shigellosis prevention and control through pathogen genomics (Preprint)
<i>Bodo saltans</i> (Kinetoplastida) is dependent on a novel <i>Paracaedibacter</i>-like endosymbiont that possesses multiple putative toxin-antitoxin systems (Journal article)
Midha, S., Rigden, D. J., Siozios, S., Hurst, G. D. D., & Jackson, A. P. (2021). <i>Bodo saltans</i> (Kinetoplastida) is dependent on a novel <i>Paracaedibacter</i>-like endosymbiont that possesses multiple putative toxin-antitoxin systems. ISME JOURNAL, 15(6), 1680-1694. doi:10.1038/s41396-020-00879-6Bisphenol A Inhibits the Transporter Function of the Blood-Brain Barrier by Directly Interacting with the ABC Transporter Breast Cancer Resistance Protein (BCRP) (Journal article)
Engdahl, E., van Schijndel, M. D. M., Voulgaris, D., Di Criscio, M., Ramsbottom, K. A., Rigden, D. J., . . . Ruegg, J. (2021). 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). doi:10.3390/ijms22115534Evaluation of model refinement in CASP14 (Preprint)
Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer (Journal article)
Edogbanya, J., Tejada-Martinez, D., Jones, N. J., Jaiswal, A., Bell, S., Cordeiro, R., . . . de Magalhaes, J. P. (2021). Evolution, structure and emerging roles of C1ORF112 in DNA replication, DNA damage responses, and cancer. CELLULAR AND MOLECULAR LIFE SCIENCES, 78(9), 4365-4376. doi:10.1007/s00018-021-03789-8Identification of unknown proteins in X-ray crystallography and cryo-EM (Preprint)
ConPlot: web-based application for the visualization of protein contact maps integrated with other data (Journal article)
Rodriguez, F. S., Mesdaghi, S., Simpkin, A. J., Burgos-Marmol, J. J., Murphy, D. L., Uski, V., . . . Rigden, D. J. (2021). ConPlot: web-based application for the visualization of protein contact maps integrated with other data. BIOINFORMATICS, 37(17), 2763-2765. doi:10.1093/bioinformatics/btab049RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis (Journal article)
Chen, K., Song, B., Tang, Y., Wei, Z., Xu, Q., Su, J., . . . Meng, J. (2021). RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. NUCLEIC ACIDS RESEARCH, 49(D1), D1396-D1404. doi:10.1093/nar/gkaa790The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection (Journal article)
Rigden, D. J., & Fernandez, X. M. (2021). The 2021 <i>Nucleic Acids Research</i> database issue and the online molecular biology database collection. NUCLEIC ACIDS RESEARCH, 49(D1), D1-D9. doi:10.1093/nar/gkaa1216m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome (Journal article)
Tang, Y., Chen, K., Song, B., Ma, J., Wu, X., Xu, Q., . . . Meng, J. (2021). m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome. NUCLEIC ACIDS RESEARCH, 49(D1), D134-D143. doi:10.1093/nar/gkaa692ConPlot: web-based application for the visualization of protein contact maps integrated with other data. (Journal article)
Rodríguez, F. S., Mesdaghi, S., Simpkin, A. J., Burgos-Mármol, J. J., Murphy, D. L., Uski, V., . . . Rigden, D. J. (2021). ConPlot: web-based application for the visualization of protein contact maps integrated with other data.. Bioinform., 37, 2763-2765.In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. (Journal article)
Mesdaghi, S., Murphy, D. L., Sánchez Rodríguez, F., Burgos-Mármol, J. J., & Rigden, D. J. (2020). In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b.. F1000Research, 9, 1395. doi:10.12688/f1000research.27676.22020
Helical ensembles outperform ideal helices in molecular replacement (Journal article)
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J. Rigden, D. (Ed.) (2017). From Protein Structure to Function with Bioinformatics. Springer Netherlands. doi:10.1007/978-94-024-1069-3Function Prediction Using Patches, Pockets and Other Surface Properties (Chapter)
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Sohn, Y. -S., Shin, H. -C., Park, W. S., Ge, J., Kim, C. H., Bok, L. L., . . . Oh, B. H. (2015). Lpg0393 of Legionella pneumophila is a guanine-nucleotide exchange factor for Rab5, Rab21 and Rab22. PLoS ONE, 10(3). doi:10.1371/journal.pone.0118683Routine phasing of coiled-coil protein crystal structures with <i>AMPLE</i> (Journal article)
Thomas, J. M. H., Keegan, R. M., Bibby, J., Winn, M. D., Mayans, O., & Rigden, D. J. (2015). Routine phasing of coiled-coil protein crystal structures with <i>AMPLE</i>. IUCRJ, 2, 198-206. doi:10.1107/S2052252515002080Exploring the speed and performance of molecular replacement with <i>AMPLE</i> using <i>QUARK ab initio</i> protein models (Journal article)
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Gonçalves, A. P., Monteiro, J., Lucchi, C., Kowbel, D. J., Cordeiro, J. M., Correia-de-Sá, P., . . . Videira, A. (2014). Extracellular calcium triggers unique transcriptional programs and modulates staurosporine-induced cell death in <i>Neurospora crassa</i>.. Microbial cell (Graz, Austria), 1(9), 289-302. doi:10.15698/mic2014.09.165Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE (Journal article)
Thomas, J., Keegan, R., Bibby, J., Winn, M., Mayans, O., & Rigden, D. (2014). Rapid molecular replacement of coiled-coil and transmembrane proteins with AMPLE. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 70, C347. doi:10.1107/S2053273314096521Evidence for Loss of a Partial Flagellar Glycolytic Pathway during Trypanosomatid Evolution (Journal article)
Brown, R. W. B., Collingridge, P. W., Gull, K., Rigden, D. J., & Ginger, M. L. (2014). Evidence for Loss of a Partial Flagellar Glycolytic Pathway during Trypanosomatid Evolution. PLOS ONE, 9(7). doi:10.1371/journal.pone.0103026Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase (Journal article)
Rigden, D. J., Eberhardt, R. Y., Gilbert, H. J., Xu, Q., Chang, Y., & Godzik, A. (2014). Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinformatics, 15. doi:10.1186/1471-2105-15-196Titin kinase is an inactive pseudokinase scaffold that supports MuRF1 recruitment to the sarcomeric M-line (Journal article)
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Sheydina, A., Eberhardt, R. Y., Rigden, D. J., Chang, Y., Li, Z., Zmasek, C., . . . Godzik, A. (2014). Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinformatics, 15. doi:10.1186/1471-2105-15-112<i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models (vol 68, pg 1622, 2012) (Journal article)
Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D., & Rigden, D. J. (2014). <i>AMPLE</i>: a cluster-and-truncate approach to solve the crystal structures of small proteins using rapidly computed <i>ab initio</i> models (vol 68, pg 1622, 2012). ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70, 1174. doi:10.1107/S1399004714006154Metabolic and Target-Site Mechanisms Combine to Confer Strong DDT Resistance in <i>Anopheles gambiae</i> (Journal article)
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Franke, B., Gasch, A., Rodriguez, D., Chami, M., Khan, M. M., Rudolf, R., . . . Mayans, O. (2014). Molecular basis for the fold organization and sarcomeric targeting of the muscle atrogin MuRF1. Open Biology, 4(3). doi:10.1098/rsob.130172Conversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis (Journal article)
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Bibby, J., Keegan, R. M., Mayans, O., Winn, M. D., & Rigden, D. J. (2013). Application of the AMPLE cluster-and-truncate approach to NMR structures for molecular replacement. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 69, 2194-2201. doi:10.1107/S0907444913018453Employing <i>in vitro</i> directed molecular evolution for the selection of α-amylase variant inhibitors with activity toward cotton boll weevil enzyme (Journal article)
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Byrne, D. P., Dart, C., & Rigden, D. J. (2012). Evaluating Caveolin Interactions: Do Proteins Interact with the Caveolin Scaffolding Domain through a Widespread Aromatic Residue-Rich Motif?. PLOS ONE, 7(9). doi:10.1371/journal.pone.0044879A cluster and truncate approach to processing<i>ab initio</i>models for molecular replacement (Journal article)
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Linford, A., Yoshimura, S. -I., Bastos, R. N., Langemeyer, L., Gerondopoulos, A., Rigden, D. J., & Barr, F. A. (2012). Rab14 and Its Exchange Factor FAM116 Link Endocytic Recycling and Adherens Junction Stability in Migrating Cells. DEVELOPMENTAL CELL, 22(5), 952-966. doi:10.1016/j.devcel.2012.04.010Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions (Journal article)
Urbe, S., Liu, H., Hayes, S. D., Heride, C., Rigden, D. J., & Clague, M. J. (2012). Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions. MOLECULAR BIOLOGY OF THE CELL, 23(6), 1095-1103. doi:10.1091/mbc.E11-08-0668Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions (Journal article)
Urbé, S., Liu, H., Hayes, S. D., Heride, C., Rigden, D. J., & Clague, M. J. (2012). Systematic survey of deubiquitinase localization identifies USP21 as a regulator of centrosome- and microtubule-associated functions. Molecular Biology of the Cell, 23(6), 1095-1103. doi:10.1091/mbc.e11-08-0668Correction: Comparative Genomics of the Anopheline Glutathione S-Transferase Epsilon Cluster (Journal article)
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Mello, L. V., Chen, X., & Rigden, D. J. (2010). Mining metagenomic data for novel domains: BACON, a new carbohydrate-binding module. FEBS LETTERS, 584(11), 2421-2426. doi:10.1016/j.febslet.2010.04.045Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation (Journal article)
Polson, H. E. J., de lartigue, J., Rigden, D. J., Reedijk, M., Urbe, S., Clague, M. J., & Tooze, S. A. (2010). Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation. AUTOPHAGY, 6(4), 506-522. doi:10.4161/auto.6.4.11863CUCU Modification of mRNA Promotes Decapping and Transcript Degradation in <i>Aspergillus nidulans</i> (Journal article)
Morozov, I. Y., Jones, M. G., Razak, A. A., Rigden, D. J., & Caddick, M. X. (2010). CUCU Modification of mRNA Promotes Decapping and Transcript Degradation in <i>Aspergillus nidulans</i>. MOLECULAR AND CELLULAR BIOLOGY, 30(2), 460-469. doi:10.1128/MCB.00997-09Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in <i>Aspergillus nidulans</i> (Journal article)
Morozov, I. Y., Jones, M. G., Spiller, D. G., Rigden, D. J., Dattenboeck, C., Novotny, R., . . . Caddick, M. X. (2010). Distinct roles for Caf1, Ccr4, Edc3 and CutA in the co-ordination of transcript deadenylation, decapping and P-body formation in <i>Aspergillus nidulans</i>. MOLECULAR MICROBIOLOGY, 76(2), 503-516. doi:10.1111/j.1365-2958.2010.07118.xIntracellular Delivery and Fate of Peptide-Capped Gold Nanoparticles (Conference Paper)
Cesbron, Y., See, V., Free, P., Nativo, P., Shaheen, U., Rigden, D. J., . . . Levy, R. (2010). Intracellular Delivery and Fate of Peptide-Capped Gold Nanoparticles. In BIOPHYSICAL JOURNAL Vol. 98 (pp. 203A). doi:10.1016/j.bpj.2009.12.10812009
Identification of novel aspartic proteases from <i>Strongyloides ratti</i> and characterisation of their evolutionary relationships, stage-specific expression and molecular structure (Journal article)
Mello, L. V., O'Meara, H., Rigden, D. J., & Paterson, S. (2009). Identification of novel aspartic proteases from <i>Strongyloides ratti</i> and characterisation of their evolutionary relationships, stage-specific expression and molecular structure. BMC GENOMICS, 10. doi:10.1186/1471-2164-10-611From Protein Structure to Function with Bioinformatics (Book)
Rigden, D. J. (Ed.) (2009). From Protein Structure to Function with Bioinformatics. Springer Netherlands. doi:10.1007/978-1-4020-9058-5Cathepsin L Digestion of Nanobioconjugates upon Endocytosis (Journal article)
See, V., Free, P., Cesbron, Y., Nativo, P., Shaheen, U., Rigden, D. J., . . . Levy, R. (2009). Cathepsin L Digestion of Nanobioconjugates upon Endocytosis. ACS NANO, 3(9), 2461-2468. doi:10.1021/nn9006994Autophagy in protists Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion (Journal article)
Rigden, D. J., Michels, P. A., & Ginger, M. L. (2009). Autophagy in protists Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion. AUTOPHAGY, 5(6), 784-794. doi:10.4161/auto.8838Molecular replacement using<i>ab initio</i>polyalanine models generated with<i>ROSETTA</i> (Journal article)
Winn, M., Rigden, D., & Keegan, R. (2009). Molecular replacement using<i>ab initio</i>polyalanine models generated with<i>ROSETTA</i>. Acta Crystallographica Section A Foundations of Crystallography, 65(a1), s163. doi:10.1107/s0108767309096664Does distant homology with Evf reveal a lipid binding site in <i>Bacillus thuringiensis</i> cytolytic toxins? (Journal article)
Rigden, D. J. (2009). Does distant homology with Evf reveal a lipid binding site in <i>Bacillus thuringiensis</i> cytolytic toxins?. FEBS LETTERS, 583(10), 1555-1560. doi:10.1016/j.febslet.2009.04.038Molecular Dynamics and Electrochemical Investigations of a pH-Responsive Peptide Monolayer (Journal article)
Doneux, T., Bouffier, L., Mello, L. V., Rigden, D. J., Kejnovska, I., Fernig, D. G., . . . Nichols, R. J. (2009). Molecular Dynamics and Electrochemical Investigations of a pH-Responsive Peptide Monolayer. JOURNAL OF PHYSICAL CHEMISTRY C, 113(16), 6792-6799. doi:10.1021/jp810859kAb initio protein modelling reveals novel human MIT domains (Journal article)
Rigden, D. J., Liu, H., Hayes, S. D., Urbe, S., & Clague, M. J. (2009). Ab initio protein modelling reveals novel human MIT domains. FEBS LETTERS, 583(5), 872-878. doi:10.1016/j.febslet.2009.02.012Identification, characterization and essentiality of the unusual peroxin 13 from <i>Trypanosoma brucei</i> (Journal article)
Verplaetse, E., Rigden, D. J., & Michels, P. A. M. (2009). Identification, characterization and essentiality of the unusual peroxin 13 from <i>Trypanosoma brucei</i>. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1793(3), 516-527. doi:10.1016/j.bbamcr.2008.12.020Autophagy in protists - Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion (Journal article)
Rigden, D. J., Michels, P. A., & Ginger, M. L. (2009). Autophagy in protists - Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion. Autophagy, 5(6), 784-794.2008
Molecular replacement using <i>ab initio</i> polyalanine models generated with <i>ROSETTA</i> (Journal article)
Rigden, D. J., Keegan, R. M., & Winn, M. D. (2008). Molecular replacement using <i>ab initio</i> polyalanine models generated with <i>ROSETTA</i>. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 64, 1288-1291. doi:10.1107/S0907444908033192Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium <i>Anoxybacillus flavithermus</i> WK1 (Journal article)
Saw, J. H., Mountain, B. W., Feng, L., Omelchenko, M. V., Hou, S., Saito, J. A., . . . Alam, M. (2008). Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium <i>Anoxybacillus flavithermus</i> WK1. GENOME BIOLOGY, 9(11). doi:10.1186/gb-2008-9-11-r161Sequence analysis of GerM and SpoVS, uncharacterized bacterial sporulation proteins with widespread phylogenetic distribution (Journal article)
Rigden, D. J., & Galperin, M. Y. (2008). Sequence analysis of GerM and SpoVS, uncharacterized bacterial sporulation proteins with widespread phylogenetic distribution. BIOINFORMATICS, 24(16), 1793-1797. doi:10.1093/bioinformatics/btn314The histidine phosphatase superfamily: structure and function (Journal article)
Rigden, D. J. (2008). The histidine phosphatase superfamily: structure and function. BIOCHEMICAL JOURNAL, 409, 333-348. doi:10.1042/BJ20071097Order within a mosaic distribution of mitochondrial <i>c</i>-type cytochrome biogenesis systems? (Journal article)
Allen, J. W. A., Jackson, A. P., Rigden, D. J., Willis, A. C., Ferguson, S. J., & Ginger, M. L. (2008). Order within a mosaic distribution of mitochondrial <i>c</i>-type cytochrome biogenesis systems?. FEBS JOURNAL, 275(10), 2385-2402. doi:10.1111/j.1742-4658.2008.06380.x2007
Jaburetox-2Ec:: An insecticidal peptide derived from an isoform of urease from the plant <i>Canaualia ensiformis</i> (Journal article)
Mulinari, F., Staniscuaski, F., Bertholdo-Vargas, L. R., Postal, M., Oliveira-Neto, O. B., Riden, D. J., . . . Carlini, C. R. (2007). Jaburetox-2Ec:: An insecticidal peptide derived from an isoform of urease from the plant <i>Canaualia ensiformis</i>. PEPTIDES, 28(10), 2042-2050. doi:10.1016/j.peptides.2007.08.009Structural flexibility in <i>Trypanosoma brucei</i> enolase revealed by X-ray crystallography and molecular dynamics (Journal article)
Navarro, M. V. D. A. S., Dias, S. M. G., Mello, L. V., Giotto, M. T. D. S., Gavalda, S., Blonski, C., . . . Rigden, D. J. (2007). Structural flexibility in <i>Trypanosoma brucei</i> enolase revealed by X-ray crystallography and molecular dynamics. FEBS JOURNAL, 274(19), 5077-5089. doi:10.1111/j.1742-4658.2007.06027.xAn unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: Surprising relationship to insect ecdysteroid phosphate phosphatase (Journal article)
Davies, L., Anderson, I. P., Turner, P. C., Shirras, A. D., Rees, H. H., & Rigden, D. J. (2007). An unsuspected ecdysteroid/steroid phosphatase activity in the key T-cell regulator, Sts-1: Surprising relationship to insect ecdysteroid phosphate phosphatase. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67(3), 720-731. doi:10.1002/prot.21357The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase (Journal article)
Yu, Z., Genest, P. -A., ter Riet, B., Sweeney, K., DiPaolo, C., Kieft, R., . . . Borst, P. (2007). The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. NUCLEIC ACIDS RESEARCH, 35(7), 2107-2115. doi:10.1093/nar/gkm049Genome-based identification and characterization of a putative mucin-binding protein from the surface of <i>Streptococcus pneumoniae</i> (Journal article)
Bumbaca, D., Littlejohn, J. E., Nayakanti, H., Lucas, A. H., Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2007). Genome-based identification and characterization of a putative mucin-binding protein from the surface of <i>Streptococcus pneumoniae</i>. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 66(3), 547-558. doi:10.1002/prot.21205Acyl carrier protein phosphodiesterase (AcpH) of <i>Escherichia coli</i> is a non-canonical member of the HD phosphatase/phosphodiesterase family (Journal article)
Thomas, J., Rigden, D. J., & Cronan, J. E. (2007). Acyl carrier protein phosphodiesterase (AcpH) of <i>Escherichia coli</i> is a non-canonical member of the HD phosphatase/phosphodiesterase family. BIOCHEMISTRY, 46(1), 129-136. doi:10.1021/bi061789e16th International Ecdysone Workshop: July 10–14, 2006, Ghent University, Belgium (Journal article)
16th International Ecdysone Workshop: July 10–14, 2006, Ghent University, Belgium (2007). Journal of insect science (Online), 7.2006
Understanding the cell in terms of structure and function: insights from structural genomics (Journal article)
Rigden, D. J. (2006). Understanding the cell in terms of structure and function: insights from structural genomics. CURRENT OPINION IN BIOTECHNOLOGY, 17(5), 457-464. doi:10.1016/j.copbio.2006.07.004Design of new benzoxazole-2-thione-derived inhibitors of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: structure of a complex with a 2-phenylindole (Journal article)
Rigden, D. J., Botzki, A., Nukui, M., Mewbourne, R. B., Lamani, E., Braun, S., . . . Jedrzejas, M. J. (2006). Design of new benzoxazole-2-thione-derived inhibitors of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: structure of a complex with a 2-phenylindole. GLYCOBIOLOGY, 16(8), 757-765. doi:10.1093/glycob/cwj116Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase (Journal article)
Romanyuk, N. D., Rigden, D. J., Vatamaniuk, O. K., Lang, A., Cahoon, R. E., Jez, J. M., & Rea, P. A. (2006). Mutagenic definition of a papain-like catalytic triad, sufficiency of the N-terminal domain for single-site core catalytic enzyme acylation, and C-terminal domain for augmentative metal activation of a eukaryotic phytochelatin synthase. PLANT PHYSIOLOGY, 141(3), 858-869. doi:10.1104/pp.106.082131Molecular Modeling and inhibitory activity of cowpea cystatin against bean bruchid pests (Journal article)
Aguiar, J. M., Franco, O. L., Rigden, D. J., Bloch, C., Monteiro, A. C. S., Flores, V. M. Q., . . . Fernandes, K. V. S. (2006). Molecular Modeling and inhibitory activity of cowpea cystatin against bean bruchid pests. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63(3), 662-670. doi:10.1002/prot.20901Alternate structural conformations of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: Insights into enzyme flexibility and underlying molecular mechanism of action (Journal article)
Rigden, D. J., Littlejohn, J. E., Joshi, H. V., de Groot, B. L., & Jedrzejas, M. J. (2006). Alternate structural conformations of <i>Streptococcus pneumoniae</i> hyaluronan lyase:: Insights into enzyme flexibility and underlying molecular mechanism of action. JOURNAL OF MOLECULAR BIOLOGY, 358(4), 1165-1178. doi:10.1016/j.jmb.2006.02.066Autophagy and related processes in trypanosomatids - Insights from genomic and bioinformatic analyses (Journal article)
Herman, M., Gillies, S., Michels, P. A., & Rigden, D. L. (2006). Autophagy and related processes in trypanosomatids - Insights from genomic and bioinformatic analyses. AUTOPHAGY, 2(2), 107-118. doi:10.4161/auto.2.2.2369Evolutionary analysis of fructose 2,6-bisphosphate metabolism (Journal article)
Michels, P. A. M., & Rigden, D. J. (2006). Evolutionary analysis of fructose 2,6-bisphosphate metabolism. IUBMB LIFE, 58(3), 133-141. doi:10.1080/152165406006882802005
Implications of a genomic search for autophagy-related genes in trypanosomatids (Journal article)
Rigden, D. J., Herman, M., Gillies, S., & Michels, P. A. M. (2005). Implications of a genomic search for autophagy-related genes in trypanosomatids. BIOCHEMICAL SOCIETY TRANSACTIONS, 33, 972-974. doi:10.1042/BST0330972Analysis of glycoside hydrolase family 98: Catalytic machinery, mechanism and a novel putative carbohydrate binding module (Journal article)
Rigden, D. J. (2005). Analysis of glycoside hydrolase family 98: Catalytic machinery, mechanism and a novel putative carbohydrate binding module. FEBS LETTERS, 579(25), 5466-5472. doi:10.1016/j.febslet.2005.09.011Implications of a genomic search for autophagy-related genes in trypanosomatids. (Journal article)
Rigden, D. J., Herman, M., Gillies, S., & Michels, P. A. M. (2005). Implications of a genomic search for autophagy-related genes in trypanosomatids.. Biochemical Society transactions, 33(Pt 5), 972-974. doi:10.1042/bst20050972Regulation of ecdysteroid signalling during <i>Drosophila</i> development:: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration (Journal article)
Takeuchi, H., Rigden, D. J., Ebrahimi, B., Turner, P. C., & Rees, H. H. (2005). Regulation of ecdysteroid signalling during <i>Drosophila</i> development:: identification, characterization and modelling of ecdysone oxidase, an enzyme involved in control of ligand concentration. BIOCHEMICAL JOURNAL, 389, 637-645. doi:10.1042/BJ20050498OMICS-related research in Latin America (Journal article)
Rigden, D. J., & Galperin, M. Y. (2005). OMICS-related research in Latin America. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 9(2), 129. doi:10.1089/omi.2005.9.1296-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in trypanosomatidae - Molecular characterization, database searches, modelling studies and evolutionary analysis (Journal article)
Chevalier, N., Bertrand, L., Rider, M. H., Opperdoes, F. R., Rigden, D. J., & Michels, P. A. M. (2005). 6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in trypanosomatidae - Molecular characterization, database searches, modelling studies and evolutionary analysis. FEBS JOURNAL, 272(14), 3542-3560. doi:10.1111/j.1742-4658.2005.04774.xAn inactivated nuclease-like domain in RecC with novel function: implications for evolution (Journal article)
Rigden, D. J. (2005). An inactivated nuclease-like domain in RecC with novel function: implications for evolution. BMC STRUCTURAL BIOLOGY, 5. doi:10.1186/1472-6807-5-9OMICS-related research in South America (Journal article)
Galperin, M. Y., & Rigden, D. J. (2005). OMICS-related research in South America. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 9(1), 1. doi:10.1089/omi.2005.9.1Characterization and functional investigation of an <i>Arabidopsis</i> cDNA encoding a homologue to the d-PGMase superfamily (Journal article)
Bourgis, F., Botha, F. C., Mani, S., Hiten, F. N., Rigden, D. J., & Verbruggen, N. (2005). Characterization and functional investigation of an <i>Arabidopsis</i> cDNA encoding a homologue to the d-PGMase superfamily. JOURNAL OF EXPERIMENTAL BOTANY, 56(414), 1129-1142. doi:10.1093/jxb/eri105Monomorphic subtelomeric DNA in the filamentous fungus, <i>Metarhizium anisopliae</i>,contains a RecQ helicase-like gene (Journal article)
Inglis, P. W., Rigden, D. J., Mello, L. V., Louis, E. J., & Valadares-Inglis, M. C. (2005). Monomorphic subtelomeric DNA in the filamentous fungus, <i>Metarhizium anisopliae</i>,contains a RecQ helicase-like gene. MOLECULAR GENETICS AND GENOMICS, 274(1), 79-90. doi:10.1007/s00438-005-1154-5Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of <i>Anticarsia gemmatalis</i> nucleopolyhedrovirus (Journal article)
Dalmolin, C. C., da Silva, F. R., Mello, L. V., Rigden, D. J., & Castro, M. E. B. (2005). Nucleotide sequence and phylogenetic analyses of the DNA polymerase gene of <i>Anticarsia gemmatalis</i> nucleopolyhedrovirus. VIRUS RESEARCH, 110(1-2), 99-109. doi:10.1016/j.virusres.2005.01.0102004
Archaea recruited D-Tyr-tRNA<SUP>Tyr</SUP> deacylase for editing in Thr-tRNA synthetase (Journal article)
Rigden, D. J. (2004). Archaea recruited D-Tyr-tRNA<SUP>Tyr</SUP> deacylase for editing in Thr-tRNA synthetase. RNA, 10(12), 1845-1851. doi:10.1261/rna.7115404L-ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor - X-ray structure and molecular modeling of enzyme-inhibitor complexes (Journal article)
Botzki, A., Rigden, D. J., Braun, S., Nukui, M., Salmen, S., Hoechstetter, J., . . . Buschauer, A. (2004). L-ascorbic acid 6-hexadecanoate, a potent hyaluronidase inhibitor - X-ray structure and molecular modeling of enzyme-inhibitor complexes. JOURNAL OF BIOLOGICAL CHEMISTRY, 279(44), 45990-45997. doi:10.1074/jbc.M406146200The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution (Journal article)
Rigden, D. J., & Galperin, M. Y. (2004). The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution. JOURNAL OF MOLECULAR BIOLOGY, 343(4), 971-984. doi:10.1016/j.jmb.2004.08.077Characterization of the ligandin site of maize glutathione S-transferase I (Journal article)
Axarli, I. A., Rigden, D. J., & Labrou, N. E. (2004). Characterization of the ligandin site of maize glutathione S-transferase I. BIOCHEMICAL JOURNAL, 382, 885-893. doi:10.1042/BJ20040298A new type of antimicrobial protein with multiple histidines from the hard tick, <i>Amblyomma hebraeum</i> (Journal article)
Lai, R., Takeuchi, H., Lomas, L. O., Jonczy, J., Rigden, D. J., Rees, H. H., & Turner, P. C. (2004). A new type of antimicrobial protein with multiple histidines from the hard tick, <i>Amblyomma hebraeum</i>. FASEB JOURNAL, 18(10), 1447-+. doi:10.1096/fj.03-1154fjeWeeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase (Journal article)
Rea, P. A., Vatamaniuk, O. K., & Rigden, D. J. (2004). Weeds, worms, and more. Papain's long-lost cousin, phytochelatin synthase. PLANT PHYSIOLOGY, 136(1), 2463-2474. doi:10.1104/pp.104.048579A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C (Journal article)
Rigden, D. J. (2004). A distant evolutionary relationship between GPI-specific phospholipase D and bacterial phosphatidylcholine-preferring phospholipase C. FEBS LETTERS, 569(1-3), 229-234. doi:10.1016/j.febslet.2004.05.071Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil <i>Anthonomus grandis</i> (Coleoptera: Curculionidae) (Journal article)
Neto, O. B. D., Batista, J. A. N., Rigden, D. J., Franco, O. L., Fragoso, R. R., Monteiro, A. C. S., . . . Grossi-De-Sá, M. F. (2004). Molecular cloning of a cysteine proteinase cDNA from the cotton boll weevil <i>Anthonomus grandis</i> (Coleoptera: Curculionidae). BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 68(6), 1235-1242. doi:10.1271/bbb.68.1235Engineering the pH-dependence of kinetic parameters of maize glutathione <i>S</i>-transferase I by site-directed mutagenesis (Journal article)
Labrou, N. E., Rigden, D. J., & Clonis, Y. D. (2004). Engineering the pH-dependence of kinetic parameters of maize glutathione <i>S</i>-transferase I by site-directed mutagenesis. BIOMOLECULAR ENGINEERING, 21(2), 61-66. doi:10.1016/j.bioeng.2003.10.002Designed chimaeric galactosyl-mimodye ligands for the purification of <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase (Journal article)
Mazitsos, C. F., Rigden, D. J., & Clonis, Y. D. (2004). Designed chimaeric galactosyl-mimodye ligands for the purification of <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase. JOURNAL OF CHROMATOGRAPHY A, 1029(1-2), 103-112. doi:10.1016/j.chroma.2003.09.048The structure-function relationship in the clostripain family of peptidases (Journal article)
Labrou, N. E., & Rigden, D. J. (2004). The structure-function relationship in the clostripain family of peptidases. EUROPEAN JOURNAL OF BIOCHEMISTRY, 271(5), 983-992. doi:10.1111/j.1432-1033.2004.04000.xA diverse family of serine protemase genes expressed in cotton boll weevil (<i>Anthonomus grandis</i>):: implications for the design of pest-resistant transgenic cotton plants (Journal article)
Oliveira-Neto, O. B., Batista, J. A. N., Rigden, D. J., Fragoso, R. R., Silva, R. O., Gomes, E. A., . . . Grossi-de-Sá, M. F. (2004). A diverse family of serine protemase genes expressed in cotton boll weevil (<i>Anthonomus grandis</i>):: implications for the design of pest-resistant transgenic cotton plants. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY, 34(9), 903-918. doi:10.1016/j.ibmb.2004.06.001A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum (Journal article)
Lai, R., Takeuchi, H., Lomas, L. O., Jonczy, J., Rigden, D. J., Rees, H. H., & Turner, P. C. (2004). A new type of antimicrobial protein with multiple histidines from the hard tick, Amblyomma hebraeum. Faseb Journal, 18(10), 162-178.Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases (Journal article)
da Silva, M. C. M., Mello, L. V., Coutinho, M. V., Rigden, D. J., Neshich, G., Chrispeels, M. J., & Grossi-De-Sá, M. F. (2004). Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases. PESQUISA AGROPECUARIA BRASILEIRA, 39(3), 201-208. doi:10.1590/S0100-204X2004000300001Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of <i>Streptococcus pneumoniae</i> (Journal article)
Bumbaca, D., Littlejohn, J. E., Nayakanti, H., Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2004). Sequence analysis and characterization of a novel fibronectin-binding repeat domain from the surface of <i>Streptococcus pneumoniae</i>. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 8(4), 341-356. doi:10.1089/omi.2004.8.341The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules (Journal article)
Rigden, D. J., Mello, L. V., & Galperin, M. Y. (2004). The PA14 domain, a conserved all-β domain in bacterial toxins, enzymes, adhesins and signaling molecules. TRENDS IN BIOCHEMICAL SCIENCES, 29(7), 335-339. doi:10.1016/j.tibs.2004.05.0022003
Structures of <i>Streptococcus pneumoniae</i> hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides -: Insights into specificity and mechanism of action (Journal article)
Rigden, D. J., & Jedrzejas, M. J. (2003). Structures of <i>Streptococcus pneumoniae</i> hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides -: Insights into specificity and mechanism of action. JOURNAL OF BIOLOGICAL CHEMISTRY, 278(50), 50596-50606. doi:10.1074/jbc.M307596200Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of <i>Brachiaria brizantha</i> (Journal article)
Rodrigues, J. C. M., Cabral, G. B., Dusi, D. M. A., de Mello, L. V., Rigden, D. J., & Carneiro, V. T. C. (2003). Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of <i>Brachiaria brizantha</i>. PLANT MOLECULAR BIOLOGY, 53(6), 745-757. doi:10.1023/B:PLAN.0000023664.21910.bdFold recognition analysis of glycosyltransferase families: further members of structural superfamilies (Journal article)
Franco, O. L., & Rigden, D. J. (2003). Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies. GLYCOBIOLOGY, 13(10), 707-712. doi:10.1093/glycob/cwg098Use of phage display to select novel cystatins specific for <i>Acanthoscelides obtectus</i> cysteine proteinases (Journal article)
Melo, F. R., Mello, M. O., Franco, O. L., Rigden, D. J., Mello, L. V., Genú, A. M., . . . Grossi-de-Sá, M. F. (2003). Use of phage display to select novel cystatins specific for <i>Acanthoscelides obtectus</i> cysteine proteinases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1651(1-2), 146-152. doi:10.1016/S1570-9639(03)00264-4The crystal structure of <i>Trypanosoma brucei</i> enolase:: Visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition (Journal article)
Giotto, M. T. D., Hannaert, V., Vertommen, D., Navarro, M. V. D. S., Rider, M. H., Michels, P. A. M., . . . Rigden, D. J. (2003). The crystal structure of <i>Trypanosoma brucei</i> enolase:: Visualisation of the inhibitory metal binding site III and potential as target for selective, irreversible inhibition. JOURNAL OF MOLECULAR BIOLOGY, 331(3), 653-665. doi:10.1016/S0022-2836(03)00752-6Genome-based identification of a carbohydrate binding module in <i>Streptococcus pneumoniae</i> hyaluronate lyase (Journal article)
Rigden, D. J., & Jedrzejas, M. J. (2003). Genome-based identification of a carbohydrate binding module in <i>Streptococcus pneumoniae</i> hyaluronate lyase. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 52(2), 203-211. doi:10.1002/prot.10405Kinetic characterization, structure modelling studies and crystallization of <i>Trypanosoma brucei</i> enolase (Journal article)
Hannaert, V., Albert, M. A., Rigden, D. J., Giotto, M. T. D., Thiemann, O., Garratt, R. C., . . . Michels, P. A. M. (2003). Kinetic characterization, structure modelling studies and crystallization of <i>Trypanosoma brucei</i> enolase. EUROPEAN JOURNAL OF BIOCHEMISTRY, 270(15), 3205-3213. doi:10.1046/j.1432-1033.2003.03692.xIdentification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families (Journal article)
Rigden, D. J., Jedrzejas, M. J., & de Mello, L. V. (2003). Identification and analysis of catalytic TIM barrel domains in seven further glycoside hydrolase families. FEBS LETTERS, 544(1-3), 103-111. doi:10.1016/s0014-5793(03)00481-2Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling (Journal article)
Rigden, D. J., Lamani, E., Mello, L. V., Littlejohn, J. E., & Jedrzejas, M. J. (2003). Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. JOURNAL OF MOLECULAR BIOLOGY, 328(4), 909-920. doi:10.1016/S0022-2836(03)00350-4Amidase domains from bacterial and phage autolysins define a family of γ-D,L-glutamate-specific amidohydrolases (Journal article)
Rigden, D. J., Jedrzejas, M. J., & Galperin, M. Y. (2003). Amidase domains from bacterial and phage autolysins define a family of γ-D,L-glutamate-specific amidohydrolases. TRENDS IN BIOCHEMICAL SCIENCES, 28(5), 230-234. doi:10.1016/S0968-0004(03)00062-8An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands (Journal article)
Rigden, D. J., Jedrzejas, M. J., & Galperin, M. Y. (2003). An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands. FEMS MICROBIOLOGY LETTERS, 221(1), 103-110. doi:10.1016/S0378-1097(03)00160-5Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase (Journal article)
Rigden, D. J. (2003). Unexpected catalytic site variation in phosphoprotein phosphatase homologues of cofactor-dependent phosphoglycerate mutase. FEBS LETTERS, 536(1-3), 77-84. doi:10.1016/S0014-5793(03)00014-0Plant-like traits associated with metabolism of <i>Trypanosoma</i> parasites (Journal article)
Hannaert, V., Saavedra, E., Duffieux, F., Szikora, J. P., Rigden, D. J., Michels, P. A. M., & Opperdoes, F. R. (2003). Plant-like traits associated with metabolism of <i>Trypanosoma</i> parasites. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(3), 1067-1071. doi:10.1073/pnas.0335769100The structure of the D49 phospholipase A<sub>2</sub> piratoxin III from <i>Bothrops pirajai</i> reveals unprecedented structural displacement of the calcium-binding loop:: possible relationship to cooperative substrate binding (Journal article)
Rigden, D. J., Hwa, L. W., Marangoni, S., Toyama, M. H., & Polikarpov, I. (2003). The structure of the D49 phospholipase A<sub>2</sub> piratoxin III from <i>Bothrops pirajai</i> reveals unprecedented structural displacement of the calcium-binding loop:: possible relationship to cooperative substrate binding. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 59, 255-262. doi:10.1107/S0907444902021467Structures of phosphate and trivanadate complexes of <i>Bacillus stearothermophilus</i> phosphatase PhoE:: Structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily (Journal article)
Rigden, D. J., Littlejohn, J. E., Henderson, K., & Jedrzejas, M. J. (2003). Structures of phosphate and trivanadate complexes of <i>Bacillus stearothermophilus</i> phosphatase PhoE:: Structural and functional analysis in the cofactor-dependent phosphoglycerate mutase superfamily. JOURNAL OF MOLECULAR BIOLOGY, 325(3), 411-420. doi:10.1016/S0022-2836(02)01229-9Analysis of structure and function of putative surface-exposed proteins encoded in the <i>Streptococcus pneumoniae</i> genome:: A bioinformatics-based approach to vaccine and drug design (Journal article)
Rigden, D. J., Galperin, M. Y., & Jedrzejas, M. J. (2003). Analysis of structure and function of putative surface-exposed proteins encoded in the <i>Streptococcus pneumoniae</i> genome:: A bioinformatics-based approach to vaccine and drug design. CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 38(2), 143-168. doi:10.1080/713609215Molecular cloning of α-amylases from cotton boll weevil, <i>Anthonomus grandis</i> and structural relations to plant inhibitors:: An approach to insect resistance (Journal article)
Oliveira-Neto, O. B., Batista, J. A. N., Rigden, D. J., Franco, O. L., Falcao, R., Fragoso, R. R., . . . Grossi-de-Sá, M. F. (2003). Molecular cloning of α-amylases from cotton boll weevil, <i>Anthonomus grandis</i> and structural relations to plant inhibitors:: An approach to insect resistance. JOURNAL OF PROTEIN CHEMISTRY, 22(1), 77-87. doi:10.1023/A:1023024012657Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands? (Journal article)
Rigden, D. J., Jedrzejas, M. J., Moroz, O. V., & Galperin, M. Y. (2003). Structural diversity of calcium-binding proteins in bacteria: single-handed EF-hands?. TRENDS IN MICROBIOLOGY, 11(7), 295-297. doi:10.1016/S0966-842X(03)00153-72002
Galactosyl-mimodye ligands for <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase -: Design, synthesis and evaluation (Journal article)
Mazitsos, C. F., Rigden, D. J., Tsoungas, P. G., & Clonis, Y. D. (2002). Galactosyl-mimodye ligands for <i>Pseudomonas fluorescens</i> β-galactose dehydrogenase -: Design, synthesis and evaluation. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(22), 5391-5405. doi:10.1046/j.1432-1033.2002.03211.xOverlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from <i>Prosopis juliflora</i> (Journal article)
Franco, O. L., de Sá, M. F. G., Sales, M. P., Mello, L. V., Oliveira, A. S., & Rigden, D. J. (2002). Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from <i>Prosopis juliflora</i>. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 49(3), 335-341. doi:10.1002/prot.10228Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues. (Journal article)
Rigden, D. J., & Franco, O. L. (2002). Beta-helical catalytic domains in glycoside hydrolase families 49, 55 and 87: domain architecture, modelling and assignment of catalytic residues.. FEBS letters, 530(1-3), 225-232. doi:10.1016/s0014-5793(02)03490-7β-Helical catalytic domains in glycoside hydrolase families 49, 55 and 87:: domain architecture, modelling and assignment of catalytic residues (Journal article)
Rigden, D. J., & Franco, O. L. (2002). β-Helical catalytic domains in glycoside hydrolase families 49, 55 and 87:: domain architecture, modelling and assignment of catalytic residues. FEBS LETTERS, 530(1-3), 225-232. doi:10.1016/S0014-5793(02)03490-7PrfA protein of <i>Bacillus</i> species:: Prediction and demonstration of endonuclease activity on DNA (Journal article)
Rigden, D. J., Setlow, P., Setlow, B., Bagyan, I., Stein, R. A., & Jedrzejas, M. J. (2002). PrfA protein of <i>Bacillus</i> species:: Prediction and demonstration of endonuclease activity on DNA. PROTEIN SCIENCE, 11(10), 2370-2381. doi:10.1110/ps.0216802<i>Leishmania donovani</i> phosphofructokinase -: Gene characterization, biochemical properties and structure-modelling studies (Journal article)
López, C., Chevalier, N., Hannaert, V., Rigden, D. J., Michels, P. A. M., & Ramirez, J. L. (2002). <i>Leishmania donovani</i> phosphofructokinase -: Gene characterization, biochemical properties and structure-modelling studies. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(16), 3978-3989. doi:10.1046/j.1432-1033.2002.03086.xInhibition of trypsin by cowpea thionin:: Characterization, molecular modeling, and docking (Journal article)
Melo, F. R., Rigden, D. J., Franco, O. L., Mello, L. V., Ary, M. B., de Sá, M. F. G., & Bloch, C. (2002). Inhibition of trypsin by cowpea thionin:: Characterization, molecular modeling, and docking. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 48(2), 311-319. doi:10.1002/prot.10142Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13 (Journal article)
Rigden, D. J. (2002). Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13. FEBS LETTERS, 523(1-3), 17-22. doi:10.1016/S0014-5793(02)02879-XGalactosyl-biomimetic dye-ligands for the purification of <i>Dactylium dendroides</i> galactose oxidase (Journal article)
Mazitsos, C. F., Rigden, D. J., Tsoungas, P. G., & Clonis, Y. D. (2002). Galactosyl-biomimetic dye-ligands for the purification of <i>Dactylium dendroides</i> galactose oxidase. JOURNAL OF CHROMATOGRAPHY A, 954(1-2), 137-150. doi:10.1016/S0021-9673(02)00176-0The putative effector-binding site of <i>Leishmania mexicana</i> pyruvate kinase studied by site-directed mutagenesis (Journal article)
Hannaert, V., Yernaux, C., Rigden, D. J., Fothergill-Gilmore, L. A., Opperdoes, F. R., & Michels, P. A. M. (2002). The putative effector-binding site of <i>Leishmania mexicana</i> pyruvate kinase studied by site-directed mutagenesis. FEBS LETTERS, 514(2-3), 255-259. doi:10.1016/S0014-5793(02)02374-8Plant α-amylase inhibitors and their interaction with insect α-amylases -: Structure, function and potential for crop protection (Journal article)
Franco, O. L., Rigden, D. J., Melo, F. R., & Grossi-de-Sá, M. F. (2002). Plant α-amylase inhibitors and their interaction with insect α-amylases -: Structure, function and potential for crop protection. EUROPEAN JOURNAL OF BIOCHEMISTRY, 269(2), 397-412. doi:10.1046/j.0014-2956.2001.02656.xStructure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> with broad specificity phosphatase activity (Journal article)
Rigden, D. J., Mello, L. V., Setlow, P., & Jedrzejas, M. J. (2002). Structure and mechanism of action of a cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> with broad specificity phosphatase activity. JOURNAL OF MOLECULAR BIOLOGY, 315(5), 1129-1143. doi:10.1006/jmbi.2001.5290Breaking the mould (Journal article)
Rigden, D. (2002). Breaking the mould. Petroleum Economist, 69(4), 4-6.Deep gas potential emerges in shallow water (Journal article)
Rigden, D. (2002). Deep gas potential emerges in shallow water. Petroleum Economist, 69(6), 7-8.Deeper and deeper (Journal article)
Rigden, D. (2002). Deeper and deeper. Petroleum Economist, 69(4), 7-8.FPSOs: Market or mirage? (Journal article)
Rigden, D. (2002). FPSOs: Market or mirage?. Petroleum Economist, 69(6), 10-11.Forging ahead (Journal article)
Rigden, D. (2002). Forging ahead. Petroleum Economist, 69(6), 34.Plant α‐amylase inhibitors and their interaction with insect α‐amylases (Journal article)
Franco, O. L., Rigden, D. J., Melo, F. R., & Grossi‐de‐Sá, M. F. (2002). Plant α‐amylase inhibitors and their interaction with insect α‐amylases. European Journal of Biochemistry, 269(2), 397-412. doi:10.1046/j.0014-2956.2001.02656.xPutative pathogenesis-related genes within <i>Solanum nigrum</i> L. var. <i>americanum</i> genome:: isolation of two genes coding for PR5-like proteins, phylogenetic and sequence analysis (Journal article)
Campos, M. A., Ribeiro, S. G., Rigden, D. J., Monte, D. C., & De Sa, M. F. G. (2002). Putative pathogenesis-related genes within <i>Solanum nigrum</i> L. var. <i>americanum</i> genome:: isolation of two genes coding for PR5-like proteins, phylogenetic and sequence analysis. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY, 61(4), 205-216. doi:10.1006/pmpp.2002.0430Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors (Journal article)
Rigden, D. J., Mosolov, V. V., & Galperin, M. Y. (2002). Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors. PROTEIN SCIENCE, 11(8), 1971-1977. doi:10.1110/ps.0207202Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments (Journal article)
Rigden, D. J. (2002). Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. PROTEIN ENGINEERING, 15(2), 65-77. doi:10.1093/protein/15.2.652001
Corrigendum to: The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin‐type fold and may have arisen by horizontal gene transfer (FEBS 25160) (Journal article)
Rigden, D. J., Monteiro, A. C. S., & Grossi de Sá, M. F. (2001). Corrigendum to: The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin‐type fold and may have arisen by horizontal gene transfer (FEBS 25160). FEBS Letters, 506(3), 296. doi:10.1016/s0014-5793(01)02933-7The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (FEBS 25160) (vol 504, pg 41, 2001) (Journal article)
Rigden, D. J., Monteiro, A. C. S., & de Sá, M. F. G. (2001). The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (FEBS 25160) (vol 504, pg 41, 2001). FEBS LETTERS, 506(3), 296. doi:10.1016/S0014-5793(01)02933-7A cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase (Journal article)
Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., & Jedrzejas, M. J. (2001). A cofactor-dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase. PROTEIN SCIENCE, 10(9), 1835-1846. doi:10.1110/ps.15701A cofactor‐dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase (Journal article)
Rigden, D. J., Bagyan, I., Lamani, E., Setlow, P., & Jedrzejas, M. J. (2001). A cofactor‐dependent phosphoglycerate mutase homolog from <i>Bacillus stearothermophilus</i> is actually a broad specificity phosphatase. Protein Science, 10(9), 1835-1846. doi:10.1110/ps.15701The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer (Journal article)
Rigden, D. J., Monteiro, A. C. S., & de Sá, M. F. G. (2001). The protease inhibitor chagasin of <i>Trypanosoma cruzi</i> adopts an immunoglobulin-type fold and may have arisen by horizontal gene transfer. FEBS LETTERS, 504(1-2), 41-44. doi:10.1016/S0014-5793(01)02753-3New family of glutathionyl-biomimetic ligands for affinity chromatography of glutathione-recognising enzymes (Journal article)
Melissis, S. C., Rigden, D. J., & Clonis, Y. D. (2001). New family of glutathionyl-biomimetic ligands for affinity chromatography of glutathione-recognising enzymes. JOURNAL OF CHROMATOGRAPHY A, 917(1-2), 29-42. doi:10.1016/S0021-9673(01)00655-0A novel heterodimeric antimicrobial peptide from the tree-frog <i>Phyllomedusa distincta</i> (Journal article)
Batista, C. V. F., Scaloni, A., Rigden, D. J., Silva, L. R., Romero, A. R., Dukor, R., . . . Bloch, C. (2001). A novel heterodimeric antimicrobial peptide from the tree-frog <i>Phyllomedusa distincta</i>. FEBS LETTERS, 494(1-2), 85-89. doi:10.1016/S0014-5793(01)02324-9Active-site characterization of <i>Candida boidinii</i> formate dehydrogenase (Journal article)
Labrou, N. E., & Rigden, D. J. (2001). Active-site characterization of <i>Candida boidinii</i> formate dehydrogenase. BIOCHEMICAL JOURNAL, 354, 455-463. doi:10.1042/0264-6021:3540455Active-site characterization of Candida boidinii formate dehydrogenase (Journal article)
LABROU, N. E., & RIGDEN, D. J. (2001). Active-site characterization of Candida boidinii formate dehydrogenase. Biochemical Journal, 354(2), 455-463. doi:10.1042/bj35404552000
Characterization of active-site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase -: Elucidation of the roles of amino acids involved in substrate binding and catalysis (Journal article)
Nairn, J., Duncan, D., Price, N. E., Kelly, S. M., Fothergill-Gilmore, L. A., Uhrinova, S., . . . Price, N. C. (2000). Characterization of active-site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase -: Elucidation of the roles of amino acids involved in substrate binding and catalysis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(24), 7065-7074. doi:10.1046/j.1432-1327.2000.01802.xCharacterization of active‐site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase (Journal article)
Nairn, J., Duncan, D., Price, N. E., Kelly, S. M., Fothergill‐Gilmore, L. A., Uhrinova, S., . . . Price, N. C. (2000). Characterization of active‐site mutants of <i>Schizosaccharomyces pombe</i> phosphoglycerate mutase. European Journal of Biochemistry, 267(24), 7065-7074. doi:10.1046/j.1432-1327.2000.01802.xPurification, biochemical characterisation and partial primary structure of a new α-amylase inhibitor from <i>Secale cereale</i> (rye) (Journal article)
Iulek, J., Franco, O. L., Silva, M., Slivinski, C. T., Bloch, C., Rigden, D. J., & de Sá, M. F. G. (2000). Purification, biochemical characterisation and partial primary structure of a new α-amylase inhibitor from <i>Secale cereale</i> (rye). INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 32(11-12), 1195-1204. doi:10.1016/S1357-2725(00)00053-4Characterization of the NAD<SUP>+</SUP> binding site of <i>Candida boidinii</i> formate dehydrogenase by affinity labelling and site-directed mutagenesis (Journal article)
Labrou, N. E., Rigden, D. J., & Clonis, Y. D. (2000). Characterization of the NAD<SUP>+</SUP> binding site of <i>Candida boidinii</i> formate dehydrogenase by affinity labelling and site-directed mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(22), 6657-6664. doi:10.1046/j.1432-1327.2000.01761.xStructural modeling of a plant disease resistance gene product domain (Journal article)
Rigden, D. J., Mello, L. V., & Bertioli, D. J. (2000). Structural modeling of a plant disease resistance gene product domain. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 41(1), 133-143. doi:3.0.CO;2-M">10.1002/1097-0134(20001001)41:1<133::AID-PROT150>3.0.CO;2-MDOI: 10.1002/1097-0134(20001001)41:1<133::AID-PROT150>3.0.CO;2-M
Activity of wheat α-amylase inhibitors towards bruchid α-amylases and structural explanation of observed specificities (Journal article)
Franco, O. L., Rigden, D. J., Melo, F. R., Bloch, C., Silva, C. P., & de Sá, M. F. G. (2000). Activity of wheat α-amylase inhibitors towards bruchid α-amylases and structural explanation of observed specificities. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(8), 2166-2173. doi:10.1046/j.1432-1327.2000.01199.xGlycerol kinase of <i>Trypanosoma brucei</i> -: Cloning, molecular characterization and mutagenesis (Journal article)
Králová, I., Rigden, D. J., Opperdoes, F. R., & Michels, P. A. M. (2000). Glycerol kinase of <i>Trypanosoma brucei</i> -: Cloning, molecular characterization and mutagenesis. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(8), 2323-2333. doi:10.1046/j.1432-1327.2000.01238.xGlycerol kinase of <i>Trypanosoma brucei</i> (Journal article)
Králová, I., Rigden, D. J., Opperdoes, F. R., & Michels, P. A. M. (2000). Glycerol kinase of <i>Trypanosoma brucei</i>. European Journal of Biochemistry, 267(8), 2323-2333. doi:10.1046/j.1432-1327.2000.01238.x<i>Trypanosoma brucei</i> contains a 2,3-bisphosphoglycerate independent phosphoglycerate mutase (Journal article)
Chevalier, N., Rigden, D. J., Van Roy, J., Opperdoes, F. R., & Michels, P. A. M. (2000). <i>Trypanosoma brucei</i> contains a 2,3-bisphosphoglycerate independent phosphoglycerate mutase. EUROPEAN JOURNAL OF BIOCHEMISTRY, 267(5), 1464-1472. doi:10.1046/j.1432-1327.2000.01145.x<i>Leishmania</i> pyruvate kinase:: the crystal structure reveals the structural basis of its unique regulatory properties (Journal article)
Fothergill-Gilmore, L. A., Rigden, D. J., Michels, P. A. M., & Phillips, S. E. V. (2000). <i>Leishmania</i> pyruvate kinase:: the crystal structure reveals the structural basis of its unique regulatory properties. BIOCHEMICAL SOCIETY TRANSACTIONS, 28, 186-190. doi:10.1042/bst0280186Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties (Journal article)
Fothergill-Gilmore, L. A., & Rigden, D. J. (2000). Leishmania pyruvate kinase: the crystal structure reveals the structural basis of its unique regulatory properties. Biochemical Society Transactions, 28(1), A12. doi:10.1042/bst028a012aDesign and synthesis of germline-based hemi-humanized single-chain Fv against the CD18 surface antigen (Journal article)
Caldas, C., Coelho, V. P. C. V., Rigden, D. J., Neschich, G., Moro, A. M., & Brígido, M. M. (2000). Design and synthesis of germline-based hemi-humanized single-chain Fv against the CD18 surface antigen. PROTEIN ENGINEERING, 13(5), 353-360. doi:10.1093/protein/13.5.353Structural modeling of a plant disease resistance gene product domain (Journal article)
Rigden, D. J., Mello, L. V., & Bertioli, D. J. (2000). Structural modeling of a plant disease resistance gene product domain. Proteins, 41(1), 133-143.1999
A structural model for the <i>rol</i>A protein and its interaction with DNA (Journal article)
Rigden, D. J., & Carneiro, M. (1999). A structural model for the <i>rol</i>A protein and its interaction with DNA. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 37(4), 697-708. doi:3.0.CO;2-Y">10.1002/(SICI)1097-0134(19991201)37:4<697::AID-PROT18>3.0.CO;2-YDOI: 10.1002/(SICI)1097-0134(19991201)37:4<697::AID-PROT18>3.0.CO;2-Y