Janet Thornton

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Dame Janet Thornton
DBE, FRS, FMedSci, HonFRSC
Plos thornton.jpg
Janet Thornton
Born Janet Maureen McLoughlin[1]
(1949-05-23) 23 May 1949 (age 69)
Nationality British
Alma mater
Known for
Spouse(s)
Alan D. Thornton (m. 1970)
[1]
Children one son, one daughter[1]
Awards
Scientific career
Fields
Institutions
Thesis The conformation of dinucleotides (1975)
Doctoral students
Other notable students
Website

Dame Janet Maureen Thornton, DBE FRS FMedSci HonFRSC (born 23 May 1949)[1] is a senior scientist at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL).[29][30][31] She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function.[5][32][33][34] She was formerly director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR.[3]

Education[edit]

After graduating in physics from the University of Nottingham, Thornton completed a master's degree in biophysics at King's College London, and a PhD in Biophysics at the National Institute for Medical Research, Mill Hill, London in 1973.[35]

Career and research[edit]

After her PhD, Thornton worked in molecular biophysics with David Chilton Phillips at the University of Oxford.[36][37] In 1978, she returned to the National Institute for Medical Research, and following that took up to a Fellowship at Birkbeck College, part of the University of London. In 1990 she was appointed Professor and Director of the Biomolecular Structure and Modeling Unit in the Department of Biochemistry and Molecular Biology at University College London and later also was appointed to the Bernal Chair in the Crystallography Department at Birkbeck College.[citation needed]

Thornton was Director of the European Bioinformatics Institute (EBI) from 2001 to 2015, on the Wellcome Trust Genome Campus at Hinxton near Cambridge. [38] She was an organiser of the Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) joint Conference in Glasgow in 2004.[39]

Thornton's work is highly interdisciplinary, interfacing with structural biology, bioinformatics, biological chemistry and chemoinformatics, amongst others. She was an early pioneer in structure validation for protein crystallography, developing the widely used ProCheck software.[40] Together with Christine Orengo, she introduced the CATH[41] classification of protein structure.[6][27][42][43][44][45][46][47][48] Her group developed a robust enzyme classification, comparison and annotation tool – the EC-BLAST[49] which calculates similarity between enzymes based on chemical reactions by capturing the bond change(s), reaction centre(s) or structural similarity between them.[50][49]

From 2008 to 2012, she co-ordinated the four-year preparatory phase of the European life sciences data infrastructure ELIXIR.[3] As of 2013 she remains on the ELIXIR board as one of EMBL's scientific delegates.[51] Her research has been funded by the Medical Research Council, the Biotechnology and Biological Sciences Research Council (BBSRC)[30][52] and the European Union.

Doctoral students and postdocs[edit]

Thornton has supervised several PhD[21] and postdoctoral researchers including Julia Fischer,[7] Shiri Freilich,[9] Alex Gutteridge,[11] Simon Hubbard,[13] Abdullah Kahraman,[15] Sergio Martinez-Cuesta,[17] Frances Pearl,[19] James Torrance,[22] Matthias Zeihm,[24] Sarah Teichmann[27] and David Tudor Jones.[26]

Awards and honours[edit]

Thornton was elected Fellow of the Royal Society (FRS) in 1999.[53] She became a member of the European Molecular Biology Organisation (EMBO) in 2000,[4] a foreign associate of the US National Academy of Sciences in 2003, and a Fellow of the Academy of Medical Sciences (FMedSci) in 2014. Thornton is an Supernumerary Fellow of Churchill College, Cambridge.[1][54] She was furthermore made an Honorary Fellow of the Royal Society of Chemistry (HonFRSC) in 2017.[55] Thornton's nomination for the Royal Society reads

Her citation on election to the Academy of Medical Sciences reads:

Thornton was appointed Commander of the Order of the British Empire (CBE) in 2000 and Dame Commander of the Order of the British Empire (DBE) in the 2012 Birthday Honours for services to bioinformatics.[58] The Times named Thornton number 86 of their "Eureka 100" British scientists in 2010.[59]

References[edit]

  1. ^ a b c d e THORNTON, Dame Janet (M.). ukwhoswho.com. Who's Who. 2015 (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc.  closed access publication – behind paywall (subscription required)
  2. ^ a b Pearl, F. M.; Bennett, C. F.; Bray, J. E.; Harrison, A. P.; Martin, N; Shepherd, A; Sillitoe, I; Thornton, J; Orengo, C. A. (2003). "The CATH database: An extended protein family resource for structural and functional genomics". Nucleic Acids Research. 31 (1): 452–5. doi:10.1093/nar/gkg062. PMC 165509Freely accessible. PMID 12520050. 
  3. ^ a b c Crosswell, L. C.; Thornton, J. M. (2012). "ELIXIR: A distributed infrastructure for European biological data". Trends in Biotechnology. 30 (5): 241–242. doi:10.1016/j.tibtech.2012.02.002. PMID 22417641. 
  4. ^ a b "The EMBO Pocket Directory" (PDF). European Molecular Biology Organization. Archived from the original on 16 March 2015. 
  5. ^ a b Zagorski, N. (2005). "Profile of Janet M. Thornton". Proceedings of the National Academy of Sciences. 102 (35): 12296–12298. Bibcode:2005PNAS..10212296Z. doi:10.1073/pnas.0505819102. PMC 1194944Freely accessible. PMID 16118281.  open access publication – free to read
  6. ^ a b Janet Thornton publications indexed by Google Scholar
  7. ^ a b Fischer, Julia (2011). Characterisation, Classification and Conformational Variability of Organic Enzyme Cofactors (PhD thesis). University of Cambridge. EThOS uk.bl.ethos.599034. 
  8. ^ Fischer, J. D.; Holliday, G. L.; Thornton, J. M. (2010). "The CoFactor database: Organic cofactors in enzyme catalysis". Bioinformatics. 26 (19): 2496–2497. doi:10.1093/bioinformatics/btq442. PMC 2944199Freely accessible. PMID 20679331. 
  9. ^ a b Freilich, Shiri (2006). Towards Relating the Evolution of the Gene Repertoire in Mammals to Tissue Specialisation (PhD thesis). University of Cambridge. EThOS uk.bl.ethos.612868. 
  10. ^ Freilich, S.; Massingham, T.; Blanc, E.; Goldovsky, L.; Thornton, J. M. (2006). "Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins". Genome Biology. 7 (10): R89. doi:10.1186/gb-2006-7-10-r89. PMC 1794571Freely accessible. PMID 17029626. 
  11. ^ a b Gutteridge, Alex (2005). Understanding the Relationship Between Enzyme Structure and Catalysis (PhD thesis). University of Cambridge. EThOS uk.bl.ethos.599808. 
  12. ^ Gutteridge, A.; Thornton, J. (2005). "Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding". Journal of Molecular Biology. 346 (1): 21–28. doi:10.1016/j.jmb.2004.11.013. PMID 15663924. 
  13. ^ a b Hubbard, Simon Jeremy (1991). Analysis of protein-protein molecular recognition (PhD thesis). University College London. EThOS uk.bl.ethos.360151. 
  14. ^ Hubbard, S. J.; Campbell, S. F.; Thornton, J. M. (1991). "Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors". Journal of Molecular Biology. 220 (2): 507–30. doi:10.1016/0022-2836(91)90027-4. PMID 1856871. 
  15. ^ a b Kahraman, Abdullah (2009). The Geometry and Physicochemistry of Protein Binding Sites and Ligands and their Detection in Electron Density Maps (PhD thesis). University of Cambridge. 
  16. ^ Kahraman, A.; Morris, R. J.; Laskowski, R. A.; Favia, A. D.; Thornton, J. M. (2010). "On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins". Proteins: Structure, Function, and Bioinformatics. 78 (5): 1120–1136. doi:10.1002/prot.22633. PMID 19927322. 
  17. ^ a b Martinez-Cuesta, Sergio (2014). The Chemistry and Evolution of Enzyme Function: Isomerases as a Case Study (PhD thesis). University of Cambridge. 
  18. ^ Martinez Cuesta, S; Furnham, N; Rahman, S. A.; Sillitoe, I; Thornton, J. M. (2014). "The evolution of enzyme function in the isomerases". Current Opinion in Structural Biology. 26: 121–30. doi:10.1016/j.sbi.2014.06.002. PMC 4139412Freely accessible. PMID 25000289.  open access publication – free to read
  19. ^ a b Pearl, Frances Mary Genevieve (1998). Protein structural analysis : helices and their interactions (PhD thesis). University College London. EThOS uk.bl.ethos.287179. 
  20. ^ Dr Frances Pearl, University of Sussex
  21. ^ a b c Anon (2014). "Publications EMBL-EBI PhD Theses". Archived from the original on 4 March 2014. 
  22. ^ a b Torrance, James (2007). The geometry and evolution of catalytic sites and metal binding sites (PhD thesis). University of Cambridge. EThOS uk.bl.ethos.612125. 
  23. ^ Torrance, J. W.; Holliday, G. L.; Mitchell, J. B. O.; Thornton, J. M. (2007). "The Geometry of Interactions between Catalytic Residues and their Substrates". Journal of Molecular Biology. 369 (4): 1140–1152. doi:10.1016/j.jmb.2007.03.055. PMID 17466330. 
  24. ^ a b Zeihm, Matthias (2013). Computational biology of longevity in model organisms (PhD thesis). University of Cambridge. 
  25. ^ Ziehm, M; Piper, M. D.; Thornton, J. M. (2013). "Analysing variation in Drosophila aging across independent experimental studies: A meta-analysis of survival data". Aging Cell. 12 (5): 917–22. doi:10.1111/acel.12123. PMC 3963443Freely accessible. PMID 23795998. 
  26. ^ a b Jones, D. T.; Taylor, W. R.; Thornton, J. M. (1992). "A new approach to protein fold recognition". Nature. 358 (6381): 86–89. Bibcode:1992Natur.358...86J. doi:10.1038/358086a0. ISSN 0028-0836. PMID 1614539. 
  27. ^ a b c Marx, V. (2014). "The Author File: Janet Thornton". Nature Methods. 11 (2): 115. doi:10.1038/nmeth.2831. 
  28. ^ Teichmann, S. A.; Rison, S. C.; Thornton, J. M.; Riley, M; Gough, J; Chothia, C (2001). "The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli". Journal of Molecular Biology. 311 (4): 693–708. doi:10.1006/jmbi.2001.4912. PMID 11518524. 
  29. ^ "Professor Dame Janet Thornton: Director, European Bioinformatics Institute". Archived from the original on 9 June 2013. 
  30. ^ a b "Great British bioscience pioneers – Professor Dame Janet Thornton". Archived from the original on 9 February 2015. 
  31. ^ Janet Thornton publications from Europe PubMed Central
  32. ^ Dean, Caroline; Osborn, Mary; Oshlack, Alicia; Thornton, Janet (2012). "Women in Science". Genome Biology. 13 (3): 148–201. doi:10.1186/gb4005. PMC 3439960Freely accessible. PMID 22405408. 
  33. ^ "Thornton Research Group Page". Archived from the original on 18 April 2011. 
  34. ^ Search Results for author Thornton JM on PubMed.
  35. ^ Thornton, Janet (1975). The conformation of dinucleotides (PhD thesis). King's College London. 
  36. ^ Thornton, J. M.; Bayley, P. M. (1976). "Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate". Biopolymers. 15 (5): 955–975. doi:10.1002/bip.1976.360150511. PMID 177120. 
  37. ^ Perkins, W. J.; Piper, E. A.; Thornton, J. (1976). "Computer techniques for conformational studies of biological molecules". Computers in Biology and Medicine. 6 (1): 23–31. doi:10.1016/0010-4825(76)90034-2. PMID 1253578. 
  38. ^ "Janet Thornton steps down". European Bioinformatics Institute. Archived from the original on 3 July 2015. 
  39. ^ ISMB-ECCB 2004
  40. ^ Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. (1993). "PROCHECK: A program to check the stereochemical quality of protein structures". Journal of Applied Crystallography. 26 (2): 283–291. doi:10.1107/S0021889892009944. 
  41. ^ Orengo, C. A.; Michie, A. D.; Jones, S.; Jones, D. T.; Swindells, M. B.; Thornton, J. M. (1997). "CATH – a hierarchic classification of protein domain structures". Structure. 5 (8): 1093–1109. doi:10.1016/S0969-2126(97)00260-8. PMID 9309224. 
  42. ^ Sibanda, B. L.; Blundell, T. L.; Thornton, J. M. (1989). "Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering". Journal of Molecular Biology. 206 (4): 759–77. doi:10.1016/0022-2836(89)90583-4. PMID 2500530. 
  43. ^ Thornton, J. M.; Singh, J; Campbell, S; Blundell, T. L. (1988). "Protein-protein recognition via side-chain interactions". Biochemical Society Transactions. 16 (6): 927–30. doi:10.1042/bst0160927. PMID 3224756. 
  44. ^ Blundell, T. L.; Sibanda, B. L.; Sternberg, M. J.; Thornton, J. M. (1987). "Knowledge-based prediction of protein structures and the design of novel molecules". Nature. 326 (6111): 347–52. Bibcode:1987Natur.326..347B. doi:10.1038/326347a0. PMID 3550471. 
  45. ^ Janet Thornton's publications indexed by the Scopus bibliographic database. (subscription required)
  46. ^ Blundell, T; Barlow, D; Borkakoti, N; Thornton, J (1983). "Solvent-induced distortions and the curvature of alpha-helices". Nature. 306 (5940): 281–3. Bibcode:1983Natur.306..281B. doi:10.1038/306281a0. PMID 6646210. 
  47. ^ Reeves, G. A.; Eilbeck, K.; Magrane, M.; O'Donovan, C.; Montecchi-Palazzi, L.; Harris, M. A.; Orchard, S.; Jimenez, R. C.; Prlic, A.; Hubbard, T. J. P.; Hermjakob, H.; Thornton, J. M. (2008). "The Protein Feature Ontology: A tool for the unification of protein feature annotations". Bioinformatics. 24 (23): 2767–2772. doi:10.1093/bioinformatics/btn528. PMC 2912506Freely accessible. PMID 18936051. 
  48. ^ Rahman, S. A.; Cuesta, S. M.; Furnham, N.; Holliday, G. L.; Thornton, J. M. (2014). "EC-BLAST: A tool to automatically search and compare enzyme reactions". Nature Methods. 11 (2): 171–4. doi:10.1038/nmeth.2803. PMC 4122987Freely accessible. PMID 24412978. 
  49. ^ a b Rahman, Syed Asad; Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L.; Thornton, Janet M. (1 February 2014). "EC-BLAST: a tool to automatically search and compare enzyme reactions". Nature Methods. 11 (2): 171–174. doi:10.1038/nmeth.2803. ISSN 1548-7091. PMC 4122987Freely accessible. PMID 24412978. 
  50. ^ Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W.; Holliday, Gemma L. (1 July 2016). "Reaction Decoder Tool (RDT): extracting features from chemical reactions". Bioinformatics. 32 (13): 2065–2066. doi:10.1093/bioinformatics/btw096. ISSN 1367-4811. PMC 4920114Freely accessible. PMID 27153692. 
  51. ^ "ELIXIR's leadership: Governance in ELIXIR's construction phase". Archived from the original on 14 October 2013. 
  52. ^ "UK Government Grants awarded to Janet Thornton". Research Councils UK. Archived from the original on 10 March 2015. 
  53. ^ "Why Prof. Thornton was awarded the FRS". London: Royal Society. Archived from the original on 12 November 2007. 
  54. ^ "Professor Dame Janet Thornton PhD, CBE, FRS, DBE, Churchill College, Cambridge". Archived from the original on 10 March 2015. 
  55. ^ "Our Honorary Fellows". Royal Society of Chemistry. Retrieved 27 February 2018. 
  56. ^ "EC/1999/34: Thornton, Janet M". London: The Royal Society. Archived from the original on 18 February 2014. 
  57. ^ "Professor Dame Janet Thornton DBE FRS FMedSci". Academy of Medical Sciences. Archived from the original on 10 March 2015. 
  58. ^ "No. 60173". The London Gazette (Supplement). 16 June 2012. p. 6. 
  59. ^ Eureka 100: the people that matter
Academic offices
Preceded by
Michael Ashburner
Graham Cameron
Director of the European Bioinformatics Institute
2001–2015
Succeeded by
Rolf Apweiler
Ewan Birney