Michelle Kuttel

 Book image

 Publications

 

JCC cover image The cover image depicts a highly-branched repeating glycogen-like polysaccharide containing 740 glucose monomers created with the CarbBuilder software. CarbBuilder is a portable command-line tool for producing three-dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide range of carbohydrate structures, from monosaccharides to large, branched polysaccharides. CarbBuilder Version 2.0, discussed on page 2098 (DOI:10.1002/jcc.24428), supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule.

 

Please contact Michelle Kuttel if you require files of any of the articles listed below.

Book Chapters

  • The Role of Molecular Modeling in Predicting Carbohydrate Antigen Conformation and Understanding Vaccine Immunogenicity. M. M. Kuttel, and N. Ravenscroft, in Carbohydrate-Based Vaccines: From Concept to Clinic. Chapter 7, 139-173 (2018) ACS Symposium Series, Vol. 1290. DOI:10.1021/bk-2018-1290.ch007

Journal Articles

  • Conformation and cross-protection in Group B Streptococcus serotype III and Streptococcus pneumoniae serotype 14: a molecular modeling study. M. M. Kuttel, and N. Ravenscroft, Pharmaceuticals, 12 (2019) 28; DOI: 10.3390/ph12010028 [Open Access]
  • Conformations of Neisseria meningitidis serogroup A and X polysaccharides: the effects of chain length and O-acetylation. J. Hlozek, M. M. Kuttel, and N. Ravenscroft, Carbohyd. Res. 465 (2018) 44–51. DOI: 10.1016/j.carres.2018.06.007
  • Genetic and structural elucidation of capsular polysaccharides from Streptococcus pneumoniae serotype 23A and 23B and comparison to serotype 23F. N. Ravenscroft, A. Omar, J. Hlozek, C. Edmonds-Smith, R. Follador, F. Serventi, M. M. Kuttel, P. Cescutti, A. Faridmoayer, Carbohyd. Res., 450: 19-29 (2017). DOI: 10.1016/j.carres.2017.08.006
  • Cross protection in Neisseria meningitides serogroups Y and W polysaccharides: a comparative conformational analysis. M. M. Kuttel, Z. Timol and N. Ravenscroft, Carbohyd. Res., 446-447: 40-47 (2017) DOI: 10.1016/j.carres.2017.05.004
  • Fluorescence and NMR spectroscopy together with molecular simulations reveal amphiphilic characteristics of a Burkholderia biofilm exopolysaccharide. M. M. Kuttel, P. Cescutti, M. Distefano and R. Rizzo, J. Biol. Chem. ,292: 11034-11042 (2017). DOI: 10.1074/jbc.M117.785048
  • CarbBuilder: Software for Building Molecular Models of Complex Oligo- and Polysaccharide Structures. M. M. Kuttel, Jonas Stahle, and Goran Widmalm, J. Comput. Chem., J. Comput. Chem., 37(22): 2098-2105 (2016). DOI: 10.1002/jcc.24428.
  • Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A. M. Kuttel, G. E. Jackson, Mpho Mfata and N. Ravenscroft, Carbohyd. Res, 406: 27-33 (2015). DOI: 10.1016/j.carres.2014.12.013
  • Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields. M. Kuttel, M. Gordon and N. Ravenscroft, Carbohyd. Res, 390: 20-27 (2014) DOI: 10.1016/j.carres.2014.02.026
  • Scalable desktop visualization of very large radio astronomy data cubes, S. Perkins, J. Questiaux, S. Finniss, R. Tyler, S. Blyth, M. M. Kuttel,New Astronomy, 30: 1–7 (2014). DOI: 10.1016/j.newast.2013.12.007
  • Towards Realistic and Interactive Sand Simulation: A GPU-based Framework., J.- P. Longmore, P. Marais, M. Kuttel, Powder Technol., 235: 983-1000 (2013). DOI: 10.1016/j.powtec.2012.10.056
  • Efficient Compression of Molecular Dynamics Trajectory Files, Patrick Marais, Julian Kenwood, Keegan Carruthers Smith, Michelle M. Kuttel, and James Gain, J. Comp. Chem., 33(27): 2131-2141 (2012) DOI: 10.1002/jcc.23050
  • Conformational properties of two exopolysaccharides produced by Inquilinus Limosus, a cystic fibrosis lung pathogen, Michelle Kuttel, Neil Ravenscroft, Michela Foschiatti, Paola Cescutti,Roberto Rizzo, Carbohyd. Res. 350: 40-48 (2012). DOI: 10.1016/j.carres.2011.12.025
  • Conformational Free Energy of Carbohydrates, Michelle Kuttel, Mini-Reviews in Organic Chemistry 8(3): 256-262 (2011)
  • Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units, Ian Tunbridge, Robert Best, James Gain and Michelle Kuttel*, Journal of Chemical Theory and Computation 6(11): 3588-3600 (2010). DOI: 10.1021/ct1003884
  • Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins, Alexander Zawaira, Marco Gallotta, Natasha Beeton-Kempen, Lauren Coulson, Patrick Marais, Michelle Kuttel, Jonathan Blackburn, Computational Biology and Chemistry 34(1): 42-52 (2010).
  • Visualisation of Cyclic and Multi-Branched Molecules with VMD, Simon Cross, Michelle M. Kuttel, John E. Stone, James E. Gain, J. Mol. Graph. Model., 28(2): 131-139 (2009). DOI: 10.1016/j.jmgm.2009.04.010
  • Conformational free energy maps for globobiose (alpha-D-Gal-(1->4)-beta-D-Gal) in implicit and explict aqueous solution, M. Kuttel, Carbohydr. Res., 343(6): 1091-1098, (2008).
  • Techniques for visualization of carbohydrate molecules, M. Kuttel, J. Gain, A. Burger and I. Eborn, J. Mol. Graph. Model., 25: 380-388, (2006).
  • Ramachandran Free Energy Surfaces for Disaccharides: Trehalose, a Case Study, M. Kuttel and K. J. Naidoo, Carbohyd. Res. 340: 875-879, (2005).
  • Free Energy Surfaces for the α(1 →4)-Glycosidic Linkage: Implications for Polysaccharide Solution Structure and Dynamics, M. Kuttel and K. J. Naidoo, J. Phys. Chem. B, 109(15):7468-7474 (2005).
  • Glycosidic Linkage Rotations Determine Amylose Stretching Mechanism, M. Kuttel and K. J. Naidoo, J. Am. Chem. Soc. 127: 12-13 (2005).
  • Carbohydrate Solution Simulations: Producing a Force Field with Experimentally-Consistent Hydroxyl Rotational Frequencies and Populations, M. Kuttel, J. W. Brady and K. J. Naidoo, J. Comput. Chem. 23(13):1236-1243 (2002).
  • Water Structuring About the Dimer and Hexamer Repeat Units of Amylose from Molecular Dynamics Computer Simulations, K. J. Naidoo and M. Kuttel, J. Comput. Chem., 22(4): 445-456 (2001).

Peer-Reviewed Conference Proceedings

  • Improving the usability of scientific software with participatory design: a new interface design for radio astronomy visualisation software, Laurisha Rampersad, Sarah Blyth, Ed Elson, Michelle M. Kuttel, SAICSIT ’17 Proceedings of the 2017 Annual Research Conference on South African Institute of Computer Scientists and Information Technologists, 26-27 September 2016, Thaba 'Nchu, South Africa, DOI: 10.1145/3129416.3129899
  • Implementation, Validation and Profiling of a Genetic Algorithm for Molecular Conformational Optimization, Victor Gueorguiev, Michelle Kuttel, Proceedings of South African Institute for Computer Scientists and Information Technologists Conference (SAICSIT 2016), 26-27 September 2016, Johannesburg, South Africa, DOI: 10.1145/2987491.2987529.
  • Effective Visualization of Tuberculosis Three-Drug Assays: A Design Study, Sunganani Silubonde, Digby Warner, Michelle Kuttel, Proceedings of South African Institute for Computer Scientists and Information Technologists Conference (SAICSIT 2016), 26-27 September 2016, Johannesburg, South Africa, DOI: 10.1145/2987491.2987501.
  • An eHealth Android Application for Mobile Analysis of Microplate Assays, James Bellairs, Jason Hlozek, Timothy Egan, Michelle Kuttel, IST-Africa 2016 Conference Proceedings, 11-13 June 2016, Durban, South Africa, ISBN: 978-1-905824-54-0. Recieved conference "Runner-up Paper award”. DOI: 10.1109/ISTAFRICA.2016.7530644
  • Comparison of effectiveness of two mobile application designs for encouraging children to read, Erin Versveld, James Foster, Michelle Kuttel, Proceedings of South African Institute for Computer Scientists and Information Technologists Conference (SAICSIT 2015), 28-30 September 2015, Stellenbosch, South Africa ,DOI: 10.1145/2815782.2815796.
  • GPU-based Acceleration of Radio Interferometry Point Source Visibility Calculations in the MEQtrees Framework Richard J. Baxter, Patrick Marais and Michelle Kuttel Astronomical Data Analysis Software and Systems XXII, ASP Conference Series , Vol 475, pages 53-59.
  • Detection of binary pulsars with GPU-accelerated sinusoidal Hough Transformations Christopher Laidler and Michelle Kuttel Astronomical Data Analysis Software and Systems XXII, ASP Conference Series , Vol 475, pages 83-87.
  • Acceleration of automated H1 source extraction. Scott Badenhorst, Sarah Blyth and Michelle Kuttel Astronomical Data Analysis Software and Systems XXII, ASP Conference Series, Vol 475, pages 45-49.
  • CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation Michelle Kuttel, Yue Mao, Goran Widmalm and Magnus Lundborg Proceedings of 7th IEEE International Conference on e-Science , 5-8 December 2011, Stockholm, Sweden, pages: 395-402 pdf (406 KB)
  • Panopticon: Scalable Monitoring System, Duncan Clough, Stefano Rivera, Michelle Kuttel, Vincent Geddes and Patrick Marais, Proceedings of South African Institute for Computer Scientists and Information Technologists Conference (SAICSIT 2010), 11-13 October 2010, Bela-Bela, South Africa, pages: 39-47.
  • Dynamic Load Balancing of Lattice Boltzmann Free-Surface Fluid Animations,A. Reid, J. Gain and M. Kuttel, Proceedings of Afrigraph2010: the 7th International Conference on Virtual Reality, Computer Graphics, Visualization and Interaction in Africa, 21-23 June 2010, Franschhoek, South Africa pdf (7MB)
  • Visualization of Solution Sets from Automated Docking of Molecular Structures, J. Jansen van Vuuren, M. Kuttel and J. Gain, Proceedings of Afrigraph2010: the 7th International Conference on Virtual Reality, Computer Graphics, Visualization and Interaction in Africa, 21-23 June 2010, Franschhoek, South Africa pdf (3MB)
  • An Electronic Health Care Cardiac Monitoring System, Gregory Chandran, Hanh Le, Michelle Kuttel, Sena Allen, and Robert Koletka, Proceedings of IEEE International Communications Conference (ICC2010), 23-27 May 2010, Cape Town, South Africa

Theses

  • Simulations of Carbohydrate Conformational Dynamics and Thermodynamics, Michelle Kuttel, PhD thesis, University of Cape Town, June 2003. pdf (9MB)
  • Developing Analytical Tools for Saccharides in Condensed Phases, Michelle Kuttel, MSc thesis, University of Cape Town, June 1999. pdf (2.3 MB)
  • For student theses, see links on alumni page.

Recent Conference Presentations

  • CARB 74: Investigating serotype cross-protection in carbohydrate vaccines: a molecular modelling approach, American Chemical Society Fall 2017 National Meeting and Expositio; Advances in Glycan Structure & Dynamics Symposium (invited talk), 20-24 August 2017,Washington D.C., USA, Michelle M. Kuttel and Neil Ravenscroft.
  • Conformation and dynamics of pneumococcal capsular polysaccharide antigens,19th European Carbohydrate Symposium, 2-7 July 2017, Barcelona, Spain Michelle M. Kuttel and Neil Ravenscroft.
  • Modelling the conformation of bacterial polysaccharide antigens, XXIII International Symposium on Glycoconjugates, 15-20 September 2015, Split, Croatia. Abstract - M. M. Kuttel*, N. Ravenscroft, Glycoconj J 32, 240 (2015).
  • Molecular modelling of Streptococcus Pneumoniae capsular polysaccharide antigens, 27th International Carbohydrate Symposium (ICS), 12-17 January 2014, Bangalore, India pdf
ICS27 UCT group photo