ISMB member publications in 2006


Dr Tracey Barrett [top]

Waters TR, Eryilmaz J, Geddes S, Barrett TE. (2006). Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA. FEBS Lett. 580(27):6423-7.

Eryilmaz J, Ceschini S, Ryan J, Geddes S, Waters TR, Barrett TE. (2006). Structural insights into the cryptic DNA-dependent ATPase activity of UvrB. J Mol Biol. 357(1):62-72.

Dr Sanjib Bhakta [top]

Anderton MC, Bhakta S, Besra GS, Jeavons P, Eltis LD, Sim E. (2006). Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG. Mol Microbiol. 59(1):181-92.


Professor Jeremy Brockes [top]

Godwin JW, Brockes JP. (2006). Regeneration, tissue injury and the immune response. J Anat. 209(4):423-32.


Professor Steve Caddick [top]

Fitzmaurice RJ, Etheridge ZC, Jumel E, Woolfson DN, Caddick S. (2006) Microwave Enhanced Diversity-Oriented Synthesis (MEDOS): Application to the Synthesis of Functionalised Flavones using Palladium Catalysed Processes. Chemical Communication, 2006, 4814-4816

Caddick,S., Muskett,F., Stoneman,R., Woolfson,D.N. (2006). Synthetic ligands for apo-Neocarzinostatin. Journal of the American Chemical Society 128, 4204-4205.

Lewis,A.K.D.K., Mok,B.J., Tocher,D.A., Wilden,J.D., Caddick,S. (2006). A New Synthesis of β-sultams from Pentafluorophenyl (PFP) Sulfonates. Organic Letters 8(24), 5513-5515.


Professor Richard Catlow [top]

To J, Sokol AA, French SA, Catlow CR, Sherwood P, van Dam HJ. (2006). Formation of heteroatom active sites in zeolites by hydrolysis and inversion. Angew Chem Int Ed Engl. 45(10):1633-8.

Sayle,T.X.T., Catlow,C.R.A., Maphanga,R.R.,Ngoepe,P.E., Sayle,D.C. (2006). Generating MnO2 nanoparticles using simulated amorphization and recrystallization. Journal of the American Chemical Society 127(37), 12828-12837.

O'Brien MG, Beale AM, Catlow CR, Weckhuysen BM. (2006). Unique organic-inorganic interactions leading to a structure-directed microporous aluminophosphate crystallization as observed with in situ Raman spectroscopy. J Am Chem Soc. 128(36):11744-5.

Grau-Crespo,R., Moreira,I.P.R., Illas,F., deLeeuw,N.H., Catlow,C.R.A. (2006). The effect of cation coordination on the properties of oxygen vacancies in FeSbO4. Journal of Materials Chemistry 16, 1943-1949.

French SA, Sokol AA, Catlow CR, Kornherr A, Nauer GE, Zifferer G. (2006). A computational investigation of the different intermediates during organoalkoxysilane hydrolysis. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 110(48):24311-7.

Hamad S, Moon C, Catlow CR, Hulme AT, Price SL. (2006). Kinetic insights into the role of the solvent in the polymorphism of 5-fluorouracil from molecular dynamics simulations. J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 110(7):3323-9.

Kornherr A, Nauer GE, Sokol AA, French SA, Catlow CR, Zifferer G. (2006). Adsorption of organosilanes at a Zn-terminated ZnO (0001) surface: molecular dynamics study. Langmuir. 22(19):8036-42.

Catlow,C.R.A., Poole,P.H., Wolynes,P.G., Finney,J.L. (2006). Simulated silica - Discussion. Philosophical Transactions of the Royal Society of London Series A - Mathematical Physical and Engineering Sciences 363(1827), 534-535.

Gomez-Hortiguela,L., Cora,F., Catlow,C.R.A., Perez-Pariente,J. (2006). Computational Study of a chiral supramolecular arrangement of structure directing molecules for the AFI structure. Physical Chemistry Chemical Physics 8, 486-493.

Khan,S., Oldman,R.J., Cora,F., Catlow,C.R.A., French,S.A., Axon,S.A. (2006). Computational modelling study of oxygen vacancies al LaCoO3 perovskite surfaces. Physical Chemistry Chemical Physics 8, 5207-5222.

Grau-Crespo,R., Cora,F., Sokol,A.A., deLeeuw,N.H., Catlow,C.R.A. (2006). Electronic structure and magnetic coupling in FeSbO4: a DFT study using hybrid functionals and GGA+U Methods. Physical Review B 73, 035116.


Professor Peter Coveney [top]


Fowler PW, Coveney PV. (2006). A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer. Biophys J. 91(2):401-10.

Gonzalez-Segredo N, Harting J, Giupponi G, Coveney PV. (2006) Stress response and structural transitions in sheared gyroidal and lamellar amphiphilic mesophases: Lattice-Boltzmann simulations. Phys Rev E Stat Nonlin Soft Matter Phys. 73(3 Pt 1):031503.

Greenwell HC, Coveney PV. (2006). Layered double hydroxide minerals as possible prebiotic information storage and transfer compounds. Orig Life Evol Biosph. 36(1):13-37.


Dr Andrew Dingley [top]

Hecht O, Dingley AJ, Schwanter A, Ozbek S, Rose-John S, Grotzinger J. (2006). The solution structure of the membrane-proximal cytokine receptor domain of the human interleukin-6 receptor. Biol Chem. 387(9):1255-9.

Lorenzen I, Dingley AJ, Jacques Y, Grotzinger J. (2006). The structure of the interleukin-15 alpha receptor and its implications for ligand binding. J Biol Chem. 281(10):6642-7.

Mysliwy J, Dingley AJ, Sedlacek R, Grotzinger J. (2006). Structural characterization and binding properties of the hemopexin-like domain of the matrixmetalloproteinase-19. Protein Expr Purif. 46(2):406-13.



Dr Snezana Djordjevic [top]


Dahmane R, Djordjevic S, Smerdu V. (2006). Adaptive potential of human biceps femoris muscle demonstrated by histochemical, immunohistochemical and mechanomyographical methods. Med Biol Eng Comput. 44(11):999-1006. Erratum in: Med Biol Eng Comput. 2007 Mar;45(3):323-4.


Dr Paul Driscoll [top]

Jia H, Bagherzadeh A, Hartzoulakis B, Jarvis A, Lohr M, Shaikh S, Aqil R, Cheng L, Tickner M, Esposito D, Harris R, Driscoll PC, Selwood DL, Zachary IC. (2006) Characterization of a bicyclic peptide neuropilin-1 (NP-1) antagonist (EG3287) reveals importance of vascular endothelial growth factor exon 8 for NP-1 binding and role of NP-1 in KDR signaling. J Biol Chem. 281(19):13493-502.

Harris R, Bayliss R, Waksman G, Driscoll PC. (2006) Resonance Assignments of the Complex between TraN and the C-terminal Domain of TraO from the Conjugative Plasmid pKM101. J Biomol NMR. 36 Suppl 5:31.

Bunney TD, Harris R, Gandarillas NL, Josephs MB, Roe SM, Sorli SC, Paterson HF, Rodrigues-Lima F, Esposito D, Ponting CP, Gierschik P, Pearl LH, Driscoll PC, Katan M. (2006) Structural and mechanistic insights into ras association domains of phospholipase C epsilon. Mol Cell. 21(4):495-507.

Reich S, Puckey LH, Cheetham CL, Harris R, Ali AA, Bhattacharyya U, Maclagan K, Powell KA, Prodromou C, Pearl LH, Driscoll PC, Savva R. (2006) Combinatorial Domain Hunting: An effective approach for the identification of soluble protein domains adaptable to high-throughput applications. Protein Sci. 15(10):2356-65.



Professor Jasminka Godovac-Zimmerman [top]

Drukier AK, Grigoriev I, Brown LR, Tomaszewski JE, Sainsbury R, Godovac-Zimmermann J. (2006) Looking for Thom's biomarkers with proteomics. J Proteome Res. 5(8): p.2046-8.

Drukier AK, Ossetrova N, Schors E, Krasik G, Grigoriev I, Koenig C, Sulkowski M, Holcman J, Brown LR, Tomaszewski JE, Schnall MD, Sainsbury R, Lokshin AE, Godovac-Zimmermann J. (2006) High-sensitivity blood-based detection of breast cancer by multi photon detection diagnostic proteomics. J Proteome Res. 5(8): p.1906-15.



Dr Helen Hailes[top]

Lafitte,V.G.H., Aliev,A.E., Horton,P.N., Hursthouse,M.B., Hailes,H.C. (2006). Highly stable cyclic dimers based on non-covalent interactions. Chemical Communications (20), 2173-2175.

Tranchant,I., Herve,A.C., Carlisle,S., Lowe,P., Slevin,C.J., Forssten,C., Dilleen,D., Williams,D.E., Tabor,A.B., Hailes,H.C., (2006). Design and Synthesis of Ferrocene Probe Molecules for Detection by Electrochemical Methods. Bioconjugate Chemistry 17(5), 1256-1264. Erratum in: Bioconj Chem. 18(6):2203

Smith,M.E., Kaulmann,U., Ward,J.M., Hailes,H.C (2006). A colorimetric assay for screening transketolase activity. Bioorganic & Medicinal Chemistry 14(20), 7062-7065. Smith M.E.B., Smithies K., Senussi T., Dalby P.A., and Hailes H.C. (2006). The First Mimetic of the Transketolase Reaction. Eur. J. Org. Chem. 1121-1123.

Lafitte,V.G.H., Aliev,A.E., Horton,P.N., Hursthouse,M.B., Bala,K., Golding,P., Hailes,H.C. (2006). Quadruply Hydrogen Bonded Cytosine Modules for Supramolecular Applications. Journal of the American Chemical Society 128(20), 6544-6545.

Writer,M., Hurley,C.A., Sarkar,S., Copeman,D.M., Wong,J.B., Odlyha,M., Jayne, Lawrence M., Tabor,A.B., McAnulty,R.J., Ayazi, Shamlou P., Hailes,H.C., Hart,S.L. (2006). Analysis and optimization of the cationic lipid component of a lipid/peptide vector formulation for enhanced transfection in vitro and in vivo. J Liposome Res. 16(4), 373-389


Professor Karl Hale [top]

Manaviazar S, Frigerio M, Bhatia GS, Hummersone MG, Aliev AE, Hale KJ. (2006) Enantioselective formal total synthesis of the antitumor macrolide bryostatin 7. Org Lett. 8(20):4477-80.


Professor Elizabeth Hounsell [top]


Alexandra Gallagher, Joseph Aduse-Opoku, Minnie Rangarajan, Nikolay Paramonov, Ahmed Hashim, Elizabeth F. Hounsell and Michael A. Curtis. (2006). PorR of Porphyromonas gingivalis is required for maturation of Arg-gingpains and synthesis of the surface anionic polysaccharide. Molec Microbiol. Submitted

Hounsell, E.F. (2006) NMR of Carbohydrates, lipids and membranes. In: RSC Specialist Reports in Nuclear Magnetic Resonance Spectroscopy 35, 362-388.

Hashmi F, Malone-Lee J and Hounsell E F (2006). Plantar Skin in Type II diabetes: An investigation of the Biochemical and Biomechanical nature of plantar epidermis. Euro.J Dermatology. 16, 23-32.



Dr Stefan Howorka [top]

Schlapak, R., P. Pammer, D. Armitage, R. Zhu, P. Hinterdorfer, M. Vaupel, T. Fruhwirth and S. Howorka (2006). Glass surfaces grafted with high-density poly(ethylene glycol) as substrates for DNA oligonucleotide microarrays. Langmuir 22 (1): 277-285.

Hesse,J., Jacak,J., Kasper,M, Regl,G., Eichberger,T., Winklmayr,M., Aberger,F., Sonnleitner,M., Schlapak,R., Howorka,S., Muresan,L., Frischauf,A.M., Schutz,G.J. (2006). RNA expression profiling at the single-molecule level. Genome Res. 16(8), 1041-1045


Professor David Jones [top]

Ebbels, T. M., Buxton, B. F. & Jones, D. T. (2006) springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'. Bioinformatics, 22, e99-e107.

Berman, H. M., Burley, S. K., Chiu, W., Sali, A., Adzhubei, A., Bourne, P.E., Bryant, S.H., Dunbrack, R.L. Jr, Fidelis, K., Frank, J., Godzik, A., Henrick, K., Joachimiak, A., Heymann, B., Jones, D., Markley, J. L., Moult, J., Montelione, G. T., Orengo, C., Rossmann, M. G., Rost, B., Saibil, H., Schwede, T., Standley, D. M. & Westbrook, J. D. (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure, 14, 1211-1217.

Lise, S., Walker-Taylor, A. & Jones, D. T. (2006) Docking protein domains in contact space. BMC Bioinformatics, 7, 310.

McGuffin, L. J., Smith R. T., Bryson, K., Sorensen, S. A. & Jones, D. T. (2006) High throughput profile-profile based fold recognition for the entire Human proteome. BMC Bioinformatics, 7, 288.

Hurwitz, N., Pellegrini-Calace, M., Jones, D.T. (2006) Towards genome-scale structure prediction for transmembrane proteins. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361:465-475.



Dr Cristopher Kay [top]

Kay, C. W. M., Elsässer, C., Bittl, R., Farrell, S. R. and Thorpe, C. (2006) Determination of the Distance between the Two Neutral Flavin Radicals in Augmenter of Liver Regeneration by Pulsed ELDOR. Journal of the American Chemical Society. 128, 76-77.

Kay, C. W. M., Mennenga, B., Görisch, H. and Bittl, R. (2006). Structure of the Pyrroloquinoline Quinone Radical in Quinoprotein Ethanol Dehydrogenase. Journal of Biological Chemistry. 281, 1470-1476

Kay, C. W. M., Mennenga, B., Görisch, H. and Bittl, R. (2006). Substrate binding in quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa studied by electron-nuclear double resonance. Proceedings of the National Academy of Sciences of the United States of America. 103(14), 5267-5272

Schnegg, A., Kay, C. W. M., Schleicher, E., Hitomi, K., Todo, T., Mobius, K. and Weber, S. (2006). The g-tensor of the flavin cofactor in (6-4) photolyase: a 360 GHz/12.8 T electron paramagnetic resonance study. Molecular Physics. 104, 1627-1633.


Dr Nick Keep [top]

Keep NH, Ward JM, Cohen-Gonsaud M, Henderson B.(2006). Wake up! Peptidoglycan lysis and bacterial non-growth states. Trends Microbiol .14(6):271-6.

Keep, N.H., Ward, J.M, Robertson, G., Cohen-Gonsaud, M. and Henderson, B.M. (2006) Bacterial resuscitation factors: revival of viable but non-culturable bacteria. Cellular and Molecular Life Sciences Online

Morris JR, Pangon L, Boutell C, Katagiri T, Keep NH, Solomon E. (2006) Genetic analysis of BRCA1 ubiquitin ligase activity and its relationship to breast cancer susceptibility. Hum Mol Genet. 15(4):599-606.


Professor John Ladbury [top]

Ababou, A., & Ladbury, J. E. (2006). A survey of the year 2004 literature on applications of isothermal titration calorimetry. Journal of Molecular Recognition. 19 , 79-89.

Grunau, A., Paine, M. J., Ladbury, J. E. & Gutierrez, A. (2006). Global effects of the energetics of coenzyme binding: NADPH controls protein interaction properties of human cytochrome P450 reductase. Biochemistry. 45 , 1421-1434.

Cliff, M. J., Harris, R., Barford, D., Ladbury, J. E. & Williams, M. A. (2006). Conformational diversity in the TPR domain-mediated interaction of protein phosphatase 5 with Hsp90. Structure. 14 , 415-426.

Beuron, F., Dreveny, I., Yuan, X., Pye, V. E., Mckeown, C., Briggs, L. C., Cliff, M. J., Kaneko, Y., Wallis, R., Isaacson, R. L., Ladbury, J. E., Matthews, S. J., Kondo, H., Zhang, X., & Freemont, P. S. (2006). Conformational changes in the AAA ATPase p97-p47 adaptor complex. EMBO J. 25 , 1967-1976.

Evans, E. J., Castro, M. A. A. O'Brien, R., Kearney, A., Walsh, H., Sparks, L. M., Tucknott, Davies, E. A., Carmo, A. M., van der Merwe, A., Stuart, D. I., Jones, E., Ladbury, J. E., Ikemizu, S., Davies, S. J. (2006). Crystal structure and binding properties of the CD2 and CD244 (2B4) binding protein CD48. Journal of Biological Chemistry. 281 , 29309-29320.

Zavaleta, J., Chinchilla, D. B., Kaddis, C. F., Martinez, K., Brown, A., Gomez, A., Pao, A., Ramirez, A., Nilapwar, S., Ladbury, J. E., & Gomez, F. A. (2006). Partial filling affinity capillary electrophoresis techniques to probe the binding of glycopeptide antibiotics to D-Ala-D-Ala terminus peptides. Journal of Capillary Electrophoresis and Microchip Technology. 9 , 101-117.

Zavaleta, J., Chinchilla, D. B., Ramirez, A., Pao, A., Martinez, K., Nilapwar, S., Ladbury, J. E., Malik, S., & Gomez, F. A. (2006). Partial filling multiple injection affinity capillary electrophoresis (PFMIACE) to estimate binding constants of receptors to ligands. Talanta – in press.

Ladbury, J. E., & Williams, M. A. (2006). Application of isothermal titration calorimetry in exploring the extended interface. In Protein Reviews Volume 4 (Dr. Zouhair Atassi, Series Editor) “Protein Interactions – Biophysical Methodology for Multi-Component Systems ”. Editor P. Schuck. Kluwer/Plenum Publishing Corporation. New York, USA. – in press .


Dr Philip Lowden [top]

Moran N., Bassani DM, Desvergne JP, Keiper S, Lowden P.A.S, Vyle J.S, Tucker J.H.R (2006). Detection of a single DNA base-pair mismatch using an anthracene-tagged fluorescent probe. Chem. Commun. (48):5003-5.

Lowden P.A.S (2006). Aziridine Natural Products: Discovery, Biological Activity and Biosynthesis. Chapter in ‘Epoxides and Aziridines in Organic Synthesis’, edited by Andrei Yudin, Wiley-VCH 2006. (BOOK CHAPTER)

Hockly E., J. Tse, A.L. Barker, D.L. Moolman, J.-L. Beunard, A.P. Revington, K. Holt, S. Sunshine, H. Moffitt, K. Sathasivam, B. Woodman, E.E. Wanker, P.A.S. Lowden, G.P. Bates (2006). Evaluation of the benzothiazole aggregation inhibitors riluzole and PGL-135 as therapeutics for Huntington's disease. Neurobiology of Disease 21, 228-236.


Professor Charles Marson [top]

Marson,C.M., Savy,P., Rioja,A.S., Mahadevan,T., Mikol,C., Veerupillai,A., Nsubuga,E., Chahwan,A., Joel,S.P. (2006). Aromatic Sulfide Inhibitors of Histone Deacetylase based on Arysulfinyl-2,4-dienoic Acid Hydroxyamides. Journal of Medicinal Chemistry 49, 800-805.

Marson CM, Saadi M. (2006) Synthesis of the penta-oxazole core of telomestatin in a convergent approach to poly-oxazole macrocycles. Org Biomol Chem. 4(21):3892-3.


Dr Andrew Martin [top]

Cuff,A.L., Martin,A.C.R. (2006). Analysing the Ability to Retain Sidechain Hydrogen-bonds in Mutant Proteins. Bioinformatics 22(12), 1464-1470.

Deevi,S.V.V., Martin,A.C.R. (2006). An extensible automated protein annotation tool: standardizing input and output using validated XML. Bioinformatics 22(3), 291-296.

Fooks,H.M., Martin,A.C.R., Woolfson,D.N.,Sessions,R.B., Hutchinson,E.G. (2006). Amino acid pairing preferences in parallel beta-sheets in proteins. Journal of Molecular Biology 356, 32-44.



Dr Nigel Martin [top]

M Hirsch, A Tucker, S Swift, N Martin, C Orengo, P Kellam, X Liu. (2006). Improved Robustness in Time Series Analysis of Gene Expression Data by Polynomial Model Based Clustering. Proc. 2nd International Symposium CompLife 2006, 1-10.

L Zamboulis, H Fan, K Belhajjame, J Siepen, A Jones, N Martin, A.Poulovasillis, S. Hubbard, S Embury, N Paton. (2006). Data Access and Integration in the ISPIDER Proteomics Grid. Proc. 3rd International Workshop Data Integration in the Life Sciences DILS 2006, 3-18.


Dr Neil McDonald [top]

Abou-Sleiman PM, Muqit MM, McDonald NQ, Yang YX, Gandhi S, Healy DG, Harvey K, Harvey RJ, Deas E, Bhatia K, Quinn N, Lees A, Latchman DS, Wood NW.(2006). A heterozygous effect for PINK1 mutations in Parkinson's disease? Ann Neurol. 60(4):414-9.

Knowles PP, Murray-Rust J, Kjaer S, Scott RP, Hanrahan S, Santoro M, Ibanez CF, McDonald NQ (2006). Structure and chemical inhibition of the RET tyrosine kinase domain. Journal of Biological Chemistry . 281(44):33577-87.


Professor Boris Mirkin [top]

I. Wasito, B. Mirkin. (2006). Nearest neighbours in least-squares data imputation algorithms with different missing patterns. Computational Statistics & Data Analysis. 50, 926-949.


Dr Carolyn Moores [top]


Moores CA, Cooper J, Wagenbach M, Ovechkina Y, Wordeman L, Milligan RA.(2006). The role of the kinesin-13 neck in microtubule depolymerization. Cell Cycle. 5(16):1812-5.

Moores CA, Milligan RA. (2006). Lucky 13 – microtubule depolymerisation by kinesin-13 motors. J Cell Sci. 119(Pt 19):3905-13.

Moores CA, Perderiset M, Kappeler C, Kain S, Drummond D, Perkins SJ, Chelly J, Cross R, Houdusse A, Francis F (2006). Distinct roles of doublecortin modulating the microtubule cytoskeleton. EMBO J. 25, 4448-4457


Professor David Moss [top]


Davies MN, Hattotuwagama CK, Moss DS, Drew MGB and Flower DR. (2006). Statistical deconvolution of enthalpic energetics contributions to MHC-peptide binding affinity. BMC Structural Biology. 6, 5.

Davies MN, Toseland CP, Moss DS and Flower DR. (2006.) Benchmarking pK(a) prediction. BMC Biochemistry. 7, 18.

Halling-Brown, M, Quartey-Papafio, R, Travers P J and Moss D S. (2006). SiPeP: A database for the prediction of tissue-specific minor histocompatibility antigens. Int. J. Immunogenetics. 33(4):289-95.


Dr Sylvia Nagl [top]


Nagl,S. (2006), Cancer Bioinformatics: From Therapy Design to Treatment,Nagl S. B. (ed.) London: Wiley's and Sons. ISBN: 0-470-86304-8. 287pp.

Nagl,S. (2006). A path to knowledge: From data to complex systems models for cancer research and treatment. Chapter 1 in Nagl,S. (ed.) Cancer Bioinformatics: From Therapy Design to Treatment. London: Wiley's & Sons, 3-27.

Nagl,S. (2006). A path to knowledge: from data to complex systems models of cancer. Chapter 1 in Sylvia Nagl (ed.) Cancer Bioninformatics From Therapy Design to Treatment. John Wiley & Sons, 1st edition, 7-24.

Nagl,S., Williams,M., El-Mehidi,N., Patkar,V., Williamson,J. (2006). Objective Bayesian nets for integrating cancer knowledge: a systems biology approach. Proceedings of the Workshop on Probabilistic Modeling and Machine Laerning in Structural and Systems Biology 44-49

Patel,M., Nagl,S. (2006). Mathematical models of cancer. Chapter 4 in Nagl,S. (ed.) Cancer Bioinformatics: From Therapy Design to Treatment. London: Wiley's & Sons, 59-93

Patel,M., Nagl,S. (2006). Mathematical models of cancer. Chapter 4 in Sylvia Nagl (ed.) Cancer Bioinformatics: From Therapy Design to Treatment. John Wiley & Sons, 1st edition, 59-93.

Toujilov,I.V., Nagl,S.B. (2006). Client's script execution in semantic web services. Conference Proceedings of the 10th International Conference on Intelligent Engineering Systems 10, 247-252


Professor Christine Orengo [top]

Reeves,G., Dallman,T., Redfern,O., Akpor,A., Orengo,C.A. (2006). Structural diversity of domain superfamilies in the CATH database. J Mol Biol 360, 725-741.

Diboun I, Wernisch L, Orengo CA, Koltzenburg M. (2006) Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 7:252.

Ranea JA, Sillero A, Thornton JM, Orengo CA. (2006) Protein superfamily evolution and the last universal common ancestor (LUCA). J Mol Evol. 63(4):513-25.

Marsden RL, Ranea JA, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, Orengo CA.(2006) Exploiting protein structure data to explore the evolution of protein function and biological complexity. Philos Trans R Soc Lond B Biol Sci. 361, 425-440.

Marsden,R., Lee,D., Maibaum,M., Yeats,C., Orengo,C.A. (2006). Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Research 34, 1066-1080.

Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA.(2006) Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res. 34, D281-284.

Berman,H. M., Burley,S. K., Chiu,W., Sali,A., Adzhubei,A., Bourne,P.E., Bryant,S.H., Dunbrack,R.L. Jr, Fidelis,K., Frank,J., Godzik,A., Henrick,K., Joachimiak,A., Heymann,B., Jones,D., Markley,J. L., Moult,J., Montelione,G. T., Orengo,C., Rossmann,M. G., Rost,B., Saibil,H., Schwede,T., Standley,D. M., Westbrook,J. D. (2006). Outcome of a workshop on archiving structural models of biological macromolecules. Structure 14, 1211-1217.


Dr Elena Orlova [top]

Tattum MH, Cohen-Krausz S, Khalili-Shirazi A, Jackson GS, Orlova EV, Collinge J, Clarke AR, Saibil HR (2006). Elongated oligomers assemble into mammalian PrP amyloid fibrils. J Mol Biol. 31;357(3):975-85.

Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA (2006). Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus revealing a potential mechanism for RNA release. J Virol. 80(21):10395-406 (Front cover)

Okorokov AL, Sherman MB, Plisson C, Grinkevich V, Sigmundsson K, Selivanova G, Milner J, Orlova EV (2006). The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity. EMBO J. 25(21): 5191–5200

Wyatt K, White H, Wang L, Bateman O, Slingsby C, Orlova EV, Wistow G (2006). Lengsin is a survivor of an ancient family of class I glutamine synthetases in eukaryotes that has undergone evolutionary re-engineering for a tissue-specific role in the vertebrate eye lens. Structure 14(2):1823-1834

White HE, Orlova EV, Chen S, Wang L, Ignatiou A, Gowen B, Stromer T, Franzmann TM, Haslbeck M, Buchner J, Saibil HR (2006). Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein hsp26. Structure 14(7),1197-1204.

Clare DK, Orlova EV, Finbow MA, Harrison MA, Findlay JB, Saibil HR (2006). An expanded and flexible form of the vacuolar ATPase membrane sector. Structure 14(7):1149-56.



Professor Steve Perkins [top]

Saunders,R.E., Goodship,T.H.J., Zipfel,P.F., Perkins,S.J. (2006). Factor H-associated haemolytic uraemic syndrome: a web database of the structural consequences of disease-associated mutations. Human Mutation 27, 21-30.

Jozsi,M., Heinen,S., Hartmann,A., Ostrowicz,C.,Hälbich,S., Richter,H., Kunert,A., Licht,C., Saunders,R.E., Perkins,S.J., Zipfel,P.F., Skerka,C. (2006). C-terminal Mutations of the Immune Regulator Factor H as Described in Patients with Atypical Haemolytic Uraemic Syndrome Show Reduced Ligand Interaction and Endothelial Cell Binding. Journal of American Society Nephrology 17, 170-177

Clark, S.J., Higman, V.A., Mulloy, B., Perkins, S.J., Lea, S.M., Sim, R. B., Day, A. J. (2006) H384 allotypic variant of factor H associated with age-related macular degeneration has different heparin-binding properties from the non-disease associated form. J. Biol. Chem. 281 , 24713-24720.

Almogren,A., Furtado,P.B., Sun,Z., Perkins,S.J., Kerr,M.A. (2006). Biochemical and structural properties of the complex between human immunoglobulin A1 and human serum albumin by X-ray and neutron scattering and analytical ultracentrifugation. Journal of Molecular Biology 356, 413-431.

Gilbert,H.E., Aslam,M., Guthridge,J.M., Holers,V.M., Perkins,S.J. (2006). Extended linkers between CR2 SCR-1 and SCR-2 and the Fc fragment in CR2-Ig by X-ray and neutron scattering, analytical ultracentrifugation and constrained molecular modelling. Journal of Molecular Biology 356, 397-412.

Gilbert, H. E., Asokan, R., Holers, V. M. & Perkins, S. J. (2006) The flexible 15 SCR extracellular domains of human complement receptor type 2 can mediate multiple ligand and antigen interactions. J. Mol. Biol. 362 , 1132-1147.

Licht, C., Heinen, S., Jozsi, M., Löschmann, I., Saunders, R. E., Perkins, S. J., Beck, B., Skerka, C., Kirschfink, M., Hoppe, B. & Zipfel, P. F. (2006) Deletion of a single amino acid (K224) in the regulatory domain of the immune inhibitor factor H reveals a novel pathomechanism for membranoproliferative glomerulonephritis Type II. Kidney Int. 70 , 42-50.

Saunders,R.E., Perkins,S.J. (2006). A user's guide to the interactive Web database of factor H-associated hemolytic uremic syndrome. Semin Thromb Hemost. 32, 160-168

Moores , C. A., Perderiset, M., Kappeler, C., Kain, S., Drummond, D., Perkins, S. J., Chelly, J., Cross, R., Houdusse, A. and Francis, F. (2006). Distinct roles of doublecortin modulating the microtubule cytoskeleton. EMBO J ., 25 , 4448-4457 .


Professor Peter Rich [top]


Osyczka A, Zhang H, Mathé C, Rich PR, Moser CC, Dutton PL. (2006) Role of the PEWY glutamate in hydroquinone-quinone oxidation-reduction catalysis in the Qo Site of cytochrome bc1. Biochemistry. 45(35):10492-503.

Iwaki, M., Puustinen, A., Wikström, M. and Rich, P.R. (2006) Structural and Chemical Changes of the Pm Intermediate of Paracoccus denitrificans Cytochrome c Oxidase Revealed by IR Spectroscopy With Labelled Tyrosines and Histidine, Biochemistry, 45, 10873 - 10885.

Marshall, D., Fisher, N., Grigic, L., Zickermann, V., Brandt, U., Shannon, R.J., Hirst, J., Lawrence, R. and Rich, P.R. (2006) ATR-FTIR redox difference spectroscopy of Yarrowia lipolytica and bovine complex I. Biochemistry, 45, 5458-5467.

Iwaki.M., Cotton, N.P.J., Quirk, P.G., Rich, P.R. and Jackson, J.B. (2006). Molecular recognition between protein and nicotinamide dinucleotide in intact, proton-translocating transhydrogenase studied by ATR-FTIR spectroscopy, J. Amer. Chem. Soc., 128, 2621-2629.

Nixon, P.J. and Rich, P.R. [2006] Chlororespiratory Pathways and Their Physiological Significance in The Structure and Function of Plastids (Wise, R. R. and Hoober, J.K., eds), chapter 12, pp. 237251, Springer, The Netherlands.


Professor David Saggerson [top]


Not yet available


Professor Helen Saibil [top]

Tilley, SJ & Saibil, HR (2006) The mechanism of pore formation by bacterial toxins. Curr Opin Struct Biol. 16, 230-236.

Clare, D, Bakkes, PJ, van Heerikhuizen, H, Saskia M van der Vies, S, Saibil, HR (2006) An expanded protein folding cage in the GroEL-gp31 complex. J Mol Biol 358, 905-911.

Vaughan, CK, Gohlke, U, Sobott, F, Good, VM, Ali, MMU, Prodromou, C, Robinson, CV, Saibil, HR & Pearl, LH (2006) Structure of an Hsp90-Cdc37-Cdk4 complex. Mol. Cell 23, 697-707.

Ranson, NA, Clare, DK, Farr, GW, Houldershaw, D, Horwich, AL & Saibil, HR (2006) Allosteric signalling of ATP hydrolysis in GroEL-GroES complexes. Nature Struct. Mol. Biol., 13, 147-152.

Tattum, MH, Cohen-Krausz, S, Khalili-Shirazi, A, Jackson, GS, Orlova, EV, Collinge, J, Clarke, AR, Saibil, HR (2006) Elongated oligomers assemble into mammalian PrP amyloid fibrils. J. Mol. Biol. 357, 975-985.

Clare, D, Orlova, EV, Finbow, MA, Harrison, MA, Findlay, JBC, Saibil, HR (2006). An expanded and flexible form of the vacuolar ATPase membrane sector. Structure 14, 1149-1156.

White, HE, Orlova, EV, Chen, S, Wang, L, Ignatiou, A, Gowen, B, Stromer, T, Franzmann, TM, Haslbeck, M, Buchner, J, & Saibil, HR (2006) Multiple distinct assemblies reveal conformational flexibility in the small heat shock protein Hsp26. Structure 14, 1197-1204.


Dr Renos Savva [top]

Reich, S., Puckey, L.H., Cheetham, C.L., Harris, R., Ali, A.E.A, Bhattacharyya, U., Maclagan, K., Powell, K.A., Prodromou, C., Pearl, L.H., Driscoll, P.C. and Savva, R. (2006). Combinatorial Domain Hunting: An effective approach for the identification of soluble protein domains adaptable to high-throughput applications. Protein Sci. 15, 2356-2365.

Krusong, K., Carpenter, L., Bellamy, S.R.W., Savva, R. and Baldwin, G.S. (2006). A comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1. Nucleic Acids. Res. 281, 4983-4992.


Dr David Selwood [top]

Matthews N, Visintin C, Hartzoulakis B, Jarvis A, Selwood DL (2006). Aurora A and B kinases as targets for cancer: will they be selective for tumors? Expert Rev Anticancer Ther. 6(1):109-20.

Jia H, Bagherzadeh A, Hartzoulakis B, Jarvis A, Löhr M, Shaikh S, Aqil R, Cheng L, Tickner M, Esposito D, Harris R, Driscoll PC, Selwood DL, Zachary IC (2006). Characterization of a bicyclic peptide neuropilin-1 (NP-1) antagonist (EG3287) reveals importance of vascular endothelial growth factor exon 8 for NP-1 binding and role of NP-1 in KDR signaling. J Biol Chem. 281(19):13493-502.


Professor Elizabeth Shephard [top]

Phillips,I.R., Shephard,E.A. (2006), Cytochrome P450 Protocols, Phillips, I.R., Shephard, E.A. (ed.) Methods in Molecular Biology series. Series edited by John M. Walker. Totowa, New Jersey: Humana Press.

Hernandez D, Phillips R, Shephard EA. (2006) Characterization of targeted mouse embryonic stem cell chromosomes: karyotyping and fluorescence in situ hybridization of metaphase spreads. Methods Mol Biol. 320:321-7.

Janmohamed A, Phillips R, Shephard EA. (2006) Determination of cellular localization of expression of flavin-containing monooxygenase genes in mouse tissues by in situ hybridization. Methods Mol Biol. 320:295-305.

Edwards M, Wong SC, Chotpadiwetkul R, Smirlis D, Phillips R, Shephard EA. (2006) Transfection of primary cultures of rat hepatocytes. Methods Mol Biol. 320:273-82.

Hernandez D, Chandan P, Janmohamed A, Phillips R, Shephard EA. (2006) Deletion of genes from the mouse genome using Cre/loxP technology. Methods Mol Biol. 320:307-19.

Hernandez D, Melidoni AN, Phillips R, Shephard EA. (2006) Microinjection of targeted embryonic stem cells and establishment of knockout mouse lines for Fmo genes. Methods Mol Biol. 320:329-41.

Janmohamed A, Thaunsukon P, Shephard EA, Phillips R. (2006) Expression of recombinant flavin-containing monooxygenases in a baculovirus/insect cell system. Methods Mol Biol. 320:39-59.

Zhou J, Shephard EA.(2006) Mutation, polymorphism and perspectives for the future of human flavin-containing monooxygenase 3. Mutat Res. 612(3):165-71. Review.


Dr Adrian Shepherd
[top]

Kabiljo, R., Stoycheva, D., Shepherd, A.J. (2007). ProSpecTome: a new tagged corpus for protein named entity recognition. In Proceedings of the Annual Meeting of the ISMB BioLINK Special Interest Group on Text Data Mining, Vienna, Austria, 19 July 2007, 24-27

Halling-Brown, M., Moss, D., Sansom, C., Shepherd, A. (2006). Web Services, Workflow & Grid Technologies for Immunoinformatics. In Proceedings of the International Congress of Immunogenomics and Immunomics (BCII2006) , Budapest, Hungary, 8-12 October 2006, 268


Dr Christine Slingsby [top]

Marin-Vinader L, Onnekink C, van Genesen ST, Slingsby C, Lubsen NH. In vivo heteromer formation. Expression of soluble betaA4-crystallin requires coexpression of a heteromeric partner. FEBS J. 273(14):3172-82.

Wyatt K, White HE, Wang L, Bateman OA, Slingsby C, Orlova EV, Wistow G. Lengsin Is a Survivor of an Ancient Family of Class I Glutamine Synthetases Re-engineered by Evolution for a Role in the Vertebrate Lens. Structure. 14(12):1823-34.


Dr Alethea Tabor [top]

Markusen,J.F., Mason,C., Hull,D.A., Town,M.A., Tabor,A.B., Clements,M., Boshoff,C.H., Dunnill,P. (2006). Behavior of adult human mesenchymal stem cells entrapped in alginate-GRGDY beads. Tissue Engineering 12(4), 821-830.

Free,P., Hurley,C.A., Kageyanna,T., Chain,B.M., Tabor,A.B. (2006). Mannose–pepstatin conjugates as targeted inhibitors of antigen processing. Organic and Biomolecular Chemistry 4, 1817-1830

Tranchant,I., Herve,A.C., Carlisle,S., Lowe,P., Slevin,C.J., Forssten,C., Dilleen,D., Williams,D.E., Tabor,A.B., Hailes,H.C., (2006). Design and Synthesis of Ferrocene Probe Molecules for Detection by Electrochemical Methods. Bioconjugate Chemistry 17(5), 1256-1264. Erratum in: Bioconj Chem. 18(6):2203

Writer,M., Hurley,C.A., Sarkar,S., Copeman,D.M., Wong,J.B., Odlyha,M., Jayne, Lawrence M., Tabor,A.B., McAnulty,R.J., Ayazi, Shamlou P., Hailes,H.C., Hart,S.L. (2006). Analysis and optimization of the cationic lipid component of a lipid/peptide vector formulation for enhanced transfection in vitro and in vivo. J Liposome Res. 16(4), 373-389


Dr Maya Topf [top]

Topf M, Baker ML, Marti-Renom MA, Chiu W and Sali A. (2006) Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting. J Mol Biol 357, 1655-1668.


Professor Gabriel Waksman [top]


JS. Pinkner, H. Remaut, F. Buelens, E. Miller, V. Akberg, N. Pemberton, M. Hedenstrom, A. Larsson, P. Seed, G. Waksman*, SJ. Hultgren* & F. Almqvist* (2006). New Class of Rationally Designed Small Compounds Inhibit Pilus Biogenesis in Uropathogenic Bacteria. Proc. Natl. Acad. Sci. USA. 103(47):17897-902.

D. Verger, E. Miller, H. Remaut, G. Waksman* and S. Hultgren* (2006). Molecular mechanism of P pilus termination in uropathogenic E.  coli. EMBO reports. 7:1228-32.

H. Remaut and G. Waksman* (2006). Protein-protein interaction through beta-strand addition. TIBS. 34:436-444.

H. Remaut, R.J. Rose, T.J. Hannan, S.J. Hultgren, S.E. Radford, A.E. Ashcroft, and G. Waksman* (2006). Donor-strand exchange in chaperone-assisted pilus assembly proceeds through a concerted b-strand displacement mechanism. Molecular Cell. 22: 831-842.

S. Hare, R. Bayliss, C. Baron, and G. Waksman* (2006). A large domain swap in the VirB11 ATPase of Brucella suis leaves the hexameric assembly intact. Journal of Molecular Biology. 360:56-66.

G. Meng, N.K. Surana, J. StGemes, and G. Waksman* (2006). Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter. EMBO Journal. 25:2297-304

A. Paschos, G. Patey,  D. Sivanesan, C. Gao, R. Bayliss, G. Waksman, D. O'Callaghan, C. Baron* (2006). Dimerization and interactions of Brucella suis VirB8 with VirB4 and VirB10 are required for its biological activity. Proceedings of the National Academy of Sciences (USA). 103(19):7252-7.

S. Geroult, S. Virdee, and G. Waksman* (2006).  The role of water in computational and experimental derivation of binding thermodynamics of SH2 domains. Chemical Biology  & Drug Design. 67:38-45.

R. Harris, R. Bayliss, G. Waksman*, and P.C. Driscoll* (2006). Resonance assignments of the complex between TraN and the C-terminal domain of TraO from the conjugative plasmid pKM101. J. Biol. NMR. 36 Suppl 5:31.


Professor Bonnie Wallace [top]


Lees, J.G., Miles, A.J., Janes, R.W., Wallace, B.A. (2006) Optimisation and development of novel methodologies for secondary structure prediction from circular dichroism spectra. BMC Bioinformatics 7:507-517.

Lees JG, Miles AJ, Wien F, Wallace BA. (2006). A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics. 22(16):1955-62.

Miles, A.J. and Wallace, B.A. (2006). Synchrotron Radiation Circular Dichroism Spectroscopy of Proteins and Applications in Structural and Functional Genomics. Chem. Soc. Reviews. 35(1):39-51.

Wallace, B.A., Whitmore, L., and Janes, R.W. (2006). The Protein Circular Dichroism Data Bank (PCDDB): A Bioinformatics and Spectroscopic Resource. Proteins. 62(1):1-3.

O'Reilly, A.O., Khambay, B.P.S., Williamson, M.S., Field, L.M., Wallace, B.A. and Davies, T.G.E. (2006). Modelling insecticide binding sites at the voltage-gated sodium channel. Biochemical Journal. 396(2):255-263.

Whitmore, L., Janes, R.W., and Wallace, B.A. (2006). Protein Circular Dichroism Data Bank (PCDDB): Data Bank and Website Design. Chirality. 18(6):426-429.

Whitmore, L. and Wallace, B.A. (2006). Peptaibols. In: The Handbook of Biologically Active Peptides. p. 83-88.


Dr Lorenz Wernisch [top]


Newton R, Hinds J, Wernisch L. (2006). A hidden markov model web application for analysing bacterial genomotyping DNA microarray experiments. Appl Bioinformatics. 5(4):211-8.

Diboun I, Wernisch L, Orengo CA, Koltzenburg M. (2006). Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics. 7:252.

Withers M, Wernisch L, dos Reis M.(2006). Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA. 12(6):933-42.

Dr Mark Williams [top]

Matthew J. Cliff, Richard Harris, David Barford, John E. Ladbury and Mark A. Williams (2006). Conformational diversity in the TPR domain mediated interaction of protein phosphatase 5 with Hsp90. Structure. 14, 415-426.



 





 
 
   
     
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