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Dr Irilenia Nobeli

Lecturer in Bioinformatics/Computational Biology

Contact details

tel: 020 3073 8014
email: i.nobeli@mail.cryst.bbk.ac.uk

Room 356, Department of Biological Sciences, main building, Malet Street, London WC1E 7HX

Research website

About Dr Irilenia Nobeli

Research interests

  • Development and application of bioinformatics and chemoinformatics methods to analyse and compare endogenous and exogenous metabolites, understand and predict molecular recognition, and predict protein function.

    Regulation of gene expression in health and disease

    The biggest surprise from studying the human genome is the versatility of RNA as a regulator of gene expression.
    We are already active in two areas involving regulation of gene expression: a) Autism (PhD student Krzysztof Szkop), where we are interested in exploring areas of the genome that have so far been mostly ignored by researchers in the area, and b) the RNA targets of FMRP, a protein implicated in mental retardation and other cognitive deficits (MSc student Andrejus Abrosimovas). We are starting to explore publicly available next-generation sequencing data (RNAseq) and are keen to collaborate with labs that share our interests and produce this data.

    Protein-small molecule and protein-protein interactions

    The group has a long history of applying computational methods (mainly docking) to identify promising leads in drug design projects, or ligands relevant to protein function.

    Projects in this area include:

    • predicting the druggability of protein-protein interactions
    • carrying out docking projects relating to either drug design or protein function
    • fragment-based approaches
    • the origin and mechanisms of binding and catalytic promiscuity.

    Read more about this work on Dr Nobeli's research group page.

Recent publications

    • Bagneris, C. DeCaen, P.G., Naylor, C.E., Pryde, D.C., Nobeli, I., Clapham, D.E., and Wallace, B.A. (2014). Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism. PNAS 111: 8428-8433. doi:10.1073/pnas.1406855111
    • Czarnecki, J., Nobeli, I., Smith, A.M., Shepherd, A.J. (2012). A Text-Mining System for Extracting Metabolic Reactions from Full-Text Articles. BMC Bioinformatics 13: 172. doi:10.1186/1471-2105-13-172.
    • Patschull, A.O.M., Gooptu, B., Ashford, P., Daviter, T., Nobeli, I. (2012). In Silico Assessment of Potential Druggable Pockets on the Surface of a1-Antitrypsin Conformers. PLoS ONE 7: e36612. doi:10.1371/journal.pone.0036612.
    • Ashford, P., Moss, D.S., Alex, A., Yeap, S.K., Povia, A., Nobeli, I.$, Williams, M.A.$ (2012). Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics 13, 39. $ Williams and Nobeli are corresponding authors.
    • Favia, A.D., Bottegoni, G., Nobeli, I., Bisignano, P., Cavalli, A. (2011). SERAPhiC: a Benchmark for in Silico Fragment-Based Drug Design. J. Chem. Inf. Model. 51, 2882-2896.
    • Patschull, A.O.M., Segu, L., Nyon, M.P., Lomas, D.A., Nobeli, I., Barrett, T.E., Gooptu, B. (2011). 1.8 Ang X-ray crystallographic structure of alpha1-antitrypsin characterizes variable features of an important site for allosteric drug design. Acta Cryst. F67, 1492-1497.
    • Chang, Y-P. et al. (2011). Targeting serpins in high-throughput and structure-based drug design. Methods in Enzymology, 501, 139-175.
    • Guzman, J.D. et al. (2011). Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics. J. Antimicrob. Chemother., 66(8), 1766-1772.
    • Macchiarulo, A., Thornton, J.M., Nobeli, I. (2009). Mapping human metabolic pathways in the small molecule chemical space. J. Chem. Inf. Model., 49, 2272-2289.
    • Gooptu, B., Miranda, E., Nobeli, I., Mallya, M., Purkiss, A., Brown, S.C., Summers, C., Phillips, R.L., Lomas, D.A., Barrett, T.E. (2009). Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design. J. Mol. Biol., 387, 857-868.
    • Nobeli, I., Favia, A., and Thornton, J.M. (2009). Protein promiscuity and its implications for biotechnology. Nat. Biotechnol., 27, 157-167.
    • Favia, A.$, Nobeli, I.$, Glaser, F., and Thornton, J.M. (2008). Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J. Mol. Biol., 375, 855-874.$ Favia and Nobeli are joint first authors.
    • Bashton, M., Nobeli, I., and Thornton, J.M. (2008). PROCOGNATE: A cognate ligand domain mapping for enzymes. Nucleic Acids Res., 36, D618-D622.

Teaching

  • Academic year 2013-14
    • Chemoinformatics (Structural Bioinformatics module, MSc Bioinformatics with Systems Biology)
    • Sequence Analysis and Genomics (MSc Bioinformatics with Systems Biology)
    • Biocomputing II (MSc Bioinformatics with Systems Biology)
    • Systems Biology (MSc Bioinformatics with Systems Biology)
    • Introduction to Bioinformatics (MSc Microbiology/ MSc Health & Disease)
    • Admissions tutor, organiser and tutor for MSc Bioinformatics with Systems Biology