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Items: 28

1.

baerhunter: An R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data.

Ozuna A, Liberto D, Joyce RM, Arnvig KB, Nobeli I.

Bioinformatics. 2019 Aug 16. pii: btz643. doi: 10.1093/bioinformatics/btz643. [Epub ahead of print]

PMID:
31418770
2.

Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis.

Schwenk S, Moores A, Nobeli I, McHugh TD, Arnvig KB.

Nucleic Acids Res. 2018 Jun 20;46(11):5837-5849. doi: 10.1093/nar/gky226.

3.

In praise of slow.

Nobeli I.

Science. 2018 Feb 2;359(6375):602. doi: 10.1126/science.359.6375.602. Epub 2018 Feb 1. No abstract available.

PMID:
29420294
5.

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder.

Szkop KJ, Cooke PIC, Humphries JA, Kalna V, Moss DS, Schuster EF, Nobeli I.

Front Mol Neurosci. 2017 Sep 13;10:279. doi: 10.3389/fnmol.2017.00279. eCollection 2017.

6.

Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence.

Smith LJ, Bochkareva A, Rolfe MD, Hunt DM, Kahramanoglou C, Braun Y, Rodgers A, Blockley A, Coade S, Lougheed KEA, Hafneh NA, Glenn SM, Crack JC, Le Brun NE, Saldanha JW, Makarov V, Nobeli I, Arnvig K, Mukamolova GV, Buxton RS, Green J.

Nucleic Acids Res. 2017 Jun 20;45(11):6600-6612. doi: 10.1093/nar/gkx406.

7.

KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing.

Lee H, Patschull AOM, Bagnéris C, Ryan H, Sanderson CM, Ebrahimi B, Nobeli I, Barrett TE.

Nucleic Acids Res. 2017 May 5;45(8):4756-4767. doi: 10.1093/nar/gkw1340.

8.

Computational modelling of the binding of arachidonic acid to the human monooxygenase CYP2J2.

Proietti G, Abelak KK, Bishop-Bailey D, Macchiarulo A, Nobeli I.

J Mol Model. 2016 Nov;22(11):279. Epub 2016 Oct 28.

PMID:
27796781
9.

Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.

Bagnéris C, DeCaen PG, Naylor CE, Pryde DC, Nobeli I, Clapham DE, Wallace BA.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8428-33. doi: 10.1073/pnas.1406855111. Epub 2014 May 21.

10.

A text-mining system for extracting metabolic reactions from full-text articles.

Czarnecki J, Nobeli I, Smith AM, Shepherd AJ.

BMC Bioinformatics. 2012 Jul 23;13:172. doi: 10.1186/1471-2105-13-172.

11.

In silico assessment of potential druggable pockets on the surface of α1-antitrypsin conformers.

Patschull AO, Gooptu B, Ashford P, Daviter T, Nobeli I.

PLoS One. 2012;7(5):e36612. doi: 10.1371/journal.pone.0036612. Epub 2012 May 8.

12.

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

Ashford P, Moss DS, Alex A, Yeap SK, Povia A, Nobeli I, Williams MA.

BMC Bioinformatics. 2012 Mar 14;13:39. doi: 10.1186/1471-2105-13-39.

13.

Therapeutic target-site variability in α1-antitrypsin characterized at high resolution.

Patschull AO, Segu L, Nyon MP, Lomas DA, Nobeli I, Barrett TE, Gooptu B.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1492-7. doi: 10.1107/S1744309111040267. Epub 2011 Nov 25.

14.

Targeting serpins in high-throughput and structure-based drug design.

Chang YP, Mahadeva R, Patschull AO, Nobeli I, Ekeowa UI, McKay AR, Thalassinos K, Irving JA, Haq I, Nyon MP, Christodoulou J, Ordóñez A, Miranda E, Gooptu B.

Methods Enzymol. 2011;501:139-75. doi: 10.1016/B978-0-12-385950-1.00008-0.

PMID:
22078534
15.

SERAPhiC: a benchmark for in silico fragment-based drug design.

Favia AD, Bottegoni G, Nobeli I, Bisignano P, Cavalli A.

J Chem Inf Model. 2011 Nov 28;51(11):2882-96. doi: 10.1021/ci2003363. Epub 2011 Oct 12.

PMID:
21936510
16.

Interaction of N-methyl-2-alkenyl-4-quinolones with ATP-dependent MurE ligase of Mycobacterium tuberculosis: antibacterial activity, molecular docking and inhibition kinetics.

Guzman JD, Wube A, Evangelopoulos D, Gupta A, Hüfner A, Basavannacharya C, Rahman MM, Thomaschitz C, Bauer R, McHugh TD, Nobeli I, Prieto JM, Gibbons S, Bucar F, Bhakta S.

J Antimicrob Chemother. 2011 Aug;66(8):1766-72. doi: 10.1093/jac/dkr203. Epub 2011 May 28.

17.

Mapping human metabolic pathways in the small molecule chemical space.

Macchiarulo A, Thornton JM, Nobeli I.

J Chem Inf Model. 2009 Oct;49(10):2272-89. doi: 10.1021/ci900196u.

PMID:
19795883
18.

Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design.

Gooptu B, Miranda E, Nobeli I, Mallya M, Purkiss A, Brown SC, Summers C, Phillips RL, Lomas DA, Barrett TE.

J Mol Biol. 2009 Apr 10;387(4):857-68. doi: 10.1016/j.jmb.2009.01.069. Epub 2009 Feb 14.

19.

Protein promiscuity and its implications for biotechnology.

Nobeli I, Favia AD, Thornton JM.

Nat Biotechnol. 2009 Feb;27(2):157-67. doi: 10.1038/nbt1519. Review.

PMID:
19204698
20.

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.

Favia AD, Nobeli I, Glaser F, Thornton JM.

J Mol Biol. 2008 Jan 18;375(3):855-74. Epub 2007 Nov 1.

PMID:
18036612
21.

PROCOGNATE: a cognate ligand domain mapping for enzymes.

Bashton M, Nobeli I, Thornton JM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D618-22. Epub 2007 Aug 24.

22.

Cognate ligand domain mapping for enzymes.

Bashton M, Nobeli I, Thornton JM.

J Mol Biol. 2006 Dec 8;364(4):836-52. Epub 2006 Sep 20.

PMID:
17034815
23.

A bioinformatician's view of the metabolome.

Nobeli I, Thornton JM.

Bioessays. 2006 May;28(5):534-45. Review.

PMID:
16615085
24.

A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli.

Nobeli I, Spriggs RV, George RA, Thornton JM.

J Mol Biol. 2005 Mar 25;347(2):415-36.

PMID:
15740750
25.

Ligand selectivity and competition between enzymes in silico.

Macchiarulo A, Nobeli I, Thornton JM.

Nat Biotechnol. 2004 Aug;22(8):1039-45.

PMID:
15286657
26.

A structure-based anatomy of the E.coli metabolome.

Nobeli I, Ponstingl H, Krissinel EB, Thornton JM.

J Mol Biol. 2003 Dec 5;334(4):697-719.

PMID:
14636597
27.

Using structural motif templates to identify proteins with DNA binding function.

Jones S, Barker JA, Nobeli I, Thornton JM.

Nucleic Acids Res. 2003 Jun 1;31(11):2811-23.

28.

On the molecular discrimination between adenine and guanine by proteins.

Nobeli I, Laskowski RA, Valdar WS, Thornton JM.

Nucleic Acids Res. 2001 Nov 1;29(21):4294-309.

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