publications

LATEST ABSTRACT
 
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  • Google Scholar profile

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  • Publications in refereed journals

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  • Szkop, K.J., Nobeli, I. (2017) Untranslated parts of genes interpreted: Making heads or tails of high-throughput transcriptomic data via computational methods. Bioessays (to appear). doi: 10.1002/bies.201700090
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  • Szkop, K.J., Cooke, P.I.C., Humphries, J.A., Kalna, V., Moss, D.S., Schuster, E.F., Nobeli, I. (2017) Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder. Frontiers in Molecular Neuroscience 10, 279. doi: 10.3389/fnmol.2017.00279
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  • Smith, L.J., Bochkareva, A., Rolfe, M.D., Hunt, D.M., Kahramanoglou, C., Braun, Y., Rodgers, A., Blockley, A., Coade, S., Lougheed, K.E.A., Hafneh, N.A., Glenn, S.M., Crack, J.C., Le Brun, N.E., Saldanha, J.W., Makarov, V., Nobeli, I., Arnvig, K., Mukamolova G.V., ,R.S., Green, J. (2017) Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence. Nucleic Acids Res. doi: 10.1093/nar/gkx406
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  • Lee H., Patschull A.O., Bagnéris ., Ryan H., Sanderson C.M., Ebrahimi B., Nobeli, I., Barrett, T.E.(2017). KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing. Nucleic Acids Res. doi: 10.1093/nar/gkw1340.
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  • Proietti G., Abelak K.K., Bishop-Bailey D., Macchiarulo A., Nobeli I. (2016). Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2. Journal of Molecular Modeling 22(11), 279.
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  • 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
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  • 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.
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  • 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. [abstract]
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  • 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. [abstract]
  • $ Williams and Nobeli are corresponding authors.
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  • 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.
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  • 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.
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  • Chang, Y-P. et al. (2011). Targeting serpins in high-throughput and structure-based drug design. Methods in Enzymology, 501, 139-175.
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  • 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. [abstract]
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  • 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.
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  • 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.
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  • Nobeli, I., Favia, A., and Thornton, J.M. (2009). Protein promiscuity and its implications for biotechnology. Nat. Biotechnol., 27, 157-167.
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  • 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.
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  • Bashton, M., Nobeli, I., and Thornton, J.M. (2008). PROCOGNATE: A cognate ligand domain mapping for enzymes. Nucleic Acids Res., 36, D618-D622.
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  • Bashton, M., Nobeli, I., and Thornton, J.M. (2006). Cognate ligand domain mapping for enzymes. J. Mol. Biol., 364, 836-852.
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  • Nobeli, I. and Thornton, J.M. (2006). A bioinformatician's view of the metabolome. Bioessays, 28, 534-545.
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  • Nobeli, I., Spriggs, R.V., George, R., and Thornton, J.M. (2005). A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E. coli. J. Mol. Biol., 347, 415-436.
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  • Macchiarulo, A., Nobeli, I., and Thornton, J.M. (2004). Ligand selectivity and competition between enzymes in silico. Nat. Biotechnol., 22, 1039-45.
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  • Nobeli, I., Ponstingl, H., Krissinel, E.B., and Thornton, J.M. (2003). A structure-based anatomy of the E. coli metabolome. J. Mol. Biol., 334, 697-71.
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  • Jones, S., Barker, J.A., Nobeli, I., and Thornton, J.M. (2003). Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res. 31, 2811-23.
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  • Nobeli, I., Laskowski, R.A., Valdar, W.S.J, and Thornton, J.M. (2001). On the molecular discrimination between adenine and guanine by proteins. Nucleic Acids Res. 29, 4294-309.
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  • Nobeli, I., Mitchell, J.B.O., Alex, A., and Thornton, J.M. (2001). Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes. J. Comput. Chem. 22, 673-88.[abstract]
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  • Novoa, J.J., Nobeli, I., Grepioni, F., and Braga, D. (2000). Are all short O--H...O contacts hydrogen bonds? A quantitative look at the nature of the O--H...O intermolecular hydrogen bonds. New J. Chem., 24, 5-8.[abstract]
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  • Nobeli, I. and Price, S.L. (1999). A non-empirical intermolecular potential for oxalic acid crystal structures. J. Phys. Chem. A, 103, 6448-57.[abstract]
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  • Nobeli, I., Price, S.L., and Wheatley, R.J. (1998). Use of molecular overlap to predict intermolecular repulsion in N--H...O hydrogen bonds. Molec. Phys., 95, 525-37.[abstract]
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  • Nobeli, I., Price, S.L., Yeoh, S.L., and Taylor, R. (1997). On the hydrogen bonding abilities of phenols and anisoles. Chem. Phys. Letts, 280, 196-202.[abstract]
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  • Nobeli, I., Price, S.L., Lommerse, J.P.M., and Taylor, R. (1997). Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles. J. Comput. Chem., 18, 2060-74. [abstract]
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  • Invited contributions

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  • Favia, A.D. and Nobeli, I. (2011). Using chemical structure to infer biological function. In :Computational Approaches in Cheminformatics and Bioinformatics. Guha, R. and Bender, A. (eds). Wiley, ISBN: 978-0-470-38441-1.
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  • Thornton, J.M., Favia, A.D., Nobeli, I., and Furnham, N. The evolution of specificity in large protein families. FEBS J., 275, 23, Suppl. 1, 2008.
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  • Nobeli, I. and Thornton, J.M. The proteome and the metabolome - a structural perspective.Peptide Revolution: Genomics, Proteomics and Therapeutics, Michael Chorev and Tomi K. Sawyer (Editors), American Peptide Society, 2003.
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  • Nobeli, I. and Thornton, J.M. Proteins, small molecules and networks. Proceedings of EuroQSAR 2002, 14th European Symposium on Quantitative Structure Activity Relationships, Bournemouth, UK, 8-13 Sep. 2002.
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  • Theses

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  • Characterising organic hydrogen bonds. PhD thesis (UCL Chemistry, 1999).
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  • IR-relevant: An information retrieval toolkit. MSc thesis (Birkbeck Computer Science, 2003).
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