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.

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.