Search

Your search keyword '"Thornton, Janet M."' showing total 1,094 results
Start Over Author "Thornton, Janet M."
1,094 results on '"Thornton, Janet M."'

2. Capturing the geometry, function, and evolution of enzymes with 3D templates

Author

Riziotis, Ioannis G. and Thornton, Janet M.

Subjects
Quantitative Biology - Biomolecules
Abstract

Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well as some exemplar cases for examining evolutionary links in enzymes. We also introduce the concept of using more than one template per structure to represent flexible sites, as an approach to better understand catalysis through snapshots captured in enzyme structures. Functional annotation from structure is an important topic that has recently resurfaced due to the new more accurate methods of protein structure prediction. Therefore, we anticipate that template-based functional site detection will be a powerful tool in the task of characterising a vast number of new protein models., Comment: 25 pages, 4 figures

Published
2022

3. A structural biology community assessment of AlphaFold2 applications

Author

Akdel, Mehmet, Pires, Douglas EV, Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O, Mészáros, Bálint, Bryant, Patrick, Good, Lydia L, Laskowski, Roman A, Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos HM, Dunham, Alistair S, Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V, Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B, Thornton, Janet M, Davey, Norman E, Stein, Amelie, Elofsson, Arne, Croll, Tristan I, and Beltrao, Pedro

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Networking and Information Technology R&D (NITRD), Generic health relevance, Computational Biology, Furylfuramide, Binding Sites, Proteins, Databases, Protein, Protein Conformation, Chemical Sciences, Medical and Health Sciences, Biophysics, Developmental Biology, Biological sciences, Biomedical and clinical sciences, Chemical sciences
Abstract

Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.

Published
2022

11. AlphaFold heralds a data-driven revolution in biology and medicine

Author

Thornton, Janet M., Laskowski, Roman A., and Borkakoti, Neera

Subjects
Artificial intelligence -- Usage, Protein structure prediction -- Methods, Proteomics -- Analysis, Biomedical engineering -- Innovations, Artificial intelligence, Biological sciences, Health
Abstract

Protein structures predicted using artificial intelligence will aid medical research, but the greatest benefit will come if clinical data can be similarly used to better understand human disease., Author(s): Janet M. Thornton [sup.1] , Roman A. Laskowski [sup.1] , Neera Borkakoti [sup.1] Author Affiliations: (1) European Bioinformatics Institute - European Molecular Biology Laboratory EMBL-EBI, South Building, Wellcome Genome [...]

Published
2021
Full Text
View/download PDF

35. The assessment and improvement of seed quality in Brassica oleracea L

Author

Thornton, Janet M.

Subjects
580, Cabbages, Brussels sprouts, Cauliflowers
Abstract

A survey of the quality of brassica seed used for commercial transplant production revealed that overall germination was high but that there was a wide range of seed vigour, as assessed by the controlled deterioration test. These vigour differences were reflected in the performance of seed in modules, the use of low quality seed resulting in problems of a reduced rate of emergence and a lack of seedling uniformity. The improvement of seed quality was considered using three approaches. First, the use of seed soakwater conductivity as a means of predicting germination was investigated for individual seeds. This proved not to be a reliable means of sorting seeds. However, the combination of controlled deterioration followed by assessment of conductivity on bulks of seeds gave a good indication of vigour and was developed as a possible rapid vigour test. Secondly, the relation between seed size and seed performance was examined. No clear relationship was found between seed size and seed quality, although, seed size had a marked effect on seedling growth, the larger seeds consistently producing taller seedlings. Thirdly, a physiological means of seed improvement was considered. Aerated hydration in water columns was successful as an invigoration treatment resulting in increased germination rate, root length of seedlings and seed vigour leading to enhanced performance in modules. These improvements were maintained after drying and storage. The optimum short-term treatment was 8 hours hydration at 25oC. The improvement could be partly attributed to germination advancement and in addition the effect of temperature, aeration and the greater improvement of aged seeds suggested that repair processes were activated during aerated hydration. Also, prolonged hydration for up to 32 hours gave an improvement such that the performance of aged seed was not significantly different to unaged seed. Finally, one possible mechanism by which aerated hydration resulted in such improvements in seed quality was investigated. DNA synthesis began approximately 24 hours earlier in unaged than in aged seed. Hydration reduced this lag phase, indicating that the onset of DNA replication was accelerated. The use of hydroxyurea, an inhibitor of DNA replication, indicated that the repair of accumulated DNA damage may have been occurring between the 16th and 32nd hours of germination.

Published
1990

43. Structural analysis of pathogenic mutations in the DYRK1A gene in patients with developmental disorders

Author

Evers, Jochem M.G., Laskowski, Roman A., Bertolli, Marta, Clayton-Smith, Jill, Deshpande, Charu, Eason, Jacqueline, Elmslie, Frances, Flinter, Frances, Gardiner, Carol, Hurst, Jane A., Kingston, Helen, Kini, Usha, Lampe, Anne K., Lim, Derek, Male, Alison, Naik, Swati, Parker, Michael J., Price, Sue, Robert, Leema, Sarkar, Ajoy, Straub, Volker, Woods, Geoff, Thornton, Janet M., and Wright, Caroline F.

Published
2017
Full Text
View/download PDF

46. Ribosomal Protein S6 Kinase 1 Signaling Regulates Mammalian Life Span

Author

Selman, Colin, Tullet, Jennifer M. A., Wieser, Daniela, Irvine, Elaine, Lingard, Steven J., Choudhury, Agharul I., Claret, Marc, Al-Qassab, Hind, Carmignac, Danielle, Ramadani, Faruk, Woods, Angela, Robinson, Iain C. A., Schuster, Eugene, Batterham, Rachel L., Kozma, Sara C., Thomas, George, Carling, David, Okkenhaug, Klaus, Thornton, Janet M., Partridge, Linda, Gems, David, and Withers, Dominic J.

Published
2009
Full Text
View/download PDF

47. The Implications of Alternative Splicing in the ENCODE Protein Complement

Author

Tress, Michael L., Martelli, Pier Luigi, Frankish, Adam, Reeves, Gabrielle A., Wesselink, Jan Jaap, Yeats, Corin, Olason, Páll Ísólfur, Albrecht, Mario, Hegyi, Hedi, Giorgetti, Alejandro, Raimondo, Domenico, Lagarde, Julien, Laskowski, Roman A., López, Gonzalo, Sadowski, Michael I., Watson, James D., Fariselli, Piero, Rossi, Ivan, Nagy, Alinda, Kai, Wang, Størling, Zenia, Orsini, Massimiliano, Assenov, Yassen, Blankenburg, Hagen, Huthmacher, Carola, Ramírez, Fidel, Schlicker, Andreas, Denoued, France, Jones, Phil, Kerrien, Samuel, Orchard, Sandra, Antonarakis, Stylianos E., Reymond, Alexandre, Birney, Ewan, Brunak, Søren, Casadio, Rita, Guigo, Roderic, Harrow, Jennifer, Hermjakob, Henning, Jones, David T., Lengauer, Thomas, Orengo, Christine A., Patthy, László, Thornton, Janet M., Tramontano, Anna, and Valencia, Alfonso

Published
2007
Full Text
View/download PDF

50. A structural biology community assessment of AlphaFold 2 applications

Author

Akdel, Mehmet, primary, Pires, Douglas E V, additional, Porta Pardo, Eduard, additional, Jänes, Jürgen, additional, Zalevsky, Arthur O, additional, Mészáros, Bálint, additional, Bryant, Patrick, additional, Good, Lydia L., additional, Laskowski, Roman A, additional, Pozzati, Gabriele, additional, Shenoy, Aditi, additional, Zhu, Wensi, additional, Kundrotas, Petras, additional, Ruiz Serra, Victoria, additional, Rodrigues, Carlos H M, additional, Dunham, Alistair S, additional, Burke, David, additional, Borkakoti, Neera, additional, Velankar, Sameer, additional, Frost, Adam, additional, Lindorff-Larsen, Kresten, additional, Valencia, Alfonso, additional, Ovchinnikov, Sergey, additional, Durairaj, Janani, additional, Ascher, David B, additional, Thornton, Janet M, additional, Davey, Norman E, additional, Stein, Amelie, additional, Elofsson, Arne, additional, Croll, Tristan I, additional, and Beltrao, Pedro, additional

Published
2021
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results