Publications
Explore SCRU research in computational science and modelling, informatics and visualization, and glycobiomedical science
Scientific Computing Research Unit research has been published over 50 times since 2008 in some of the most respected peer-reviewed journals in the world, covering a range of fields from computational chemistry and bioinformatics to molecular simulation, physics and carbohydrate research.
Papers are researched and written by both SCRU faculty and students using the state-of-the-art facilities and tools available in the SCRU labs.
Access the publications of SCRU research in computational science and modelling, informatics and visualisation, and glycobiomedical science.
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Biomed Software Development
CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform
H.E. Kaya, K.J. Naidoo, Bioinformatics, 2023, 39(12), btad745Enzyme Reaction Dynamics From Adaptive Reaction Coordinate Forces
K.J. Naidoo, T. Bruce-Chwatt, T. Senapathi, Elsevier, 2023, volume 3, 544-558.Molecular mechanisms from reaction coordinate graph enabled multidimensional free energies illustrated on water dimer hydrogen bonding
T. Bruce-Chwatt, K.J. Naidoo, Journal of Computational Chemistry, 43, 2022, 1802-1813.Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms
K.J. Naidoo, T. Bruce-Chwatt, T. Senapathi, M. Hillebrand, Acc. Chem. Res. 2021, 54, 4120−4130.Anisotropic numerical potentials for coarse-grained modeling from high-speed multidimensional lookup table and interpolation algorithms
A. Gangopadhyay, S. Winberg, K. J. Naidoo, Journal of Computational Chemistry. 2021, 42, 666-675.Quantum supercharger library: Hyper-parallelism of the Hartree–Fock method
K.D. Fernandes, C.A. Renison and K.J. Naidoo. Journal of Computational Chemistry, 36, 2015 1399-1409.Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics
C.A. Renison, K.D. Fernandes and K.J. Naidoo. Journal of Computational Chemistry, 36, 2015 1410-1419.Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary
W. Crous, M.J. Field, K.J. Naidoo, Journal Chem. Theory Comput., 10, 2014, 1727-1738.AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems
K. Govender, J. Gao, K.J. Naidoo, Journal Chem. Theory Comput., 10, 2014, 4694-4707.Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations
K.K. Govender, K.J. Naidoo, J. Chem Theory Comput., 10 2014, 4708-4717.Interpreting medium ring canonical conformers by a triangular plane tessellation of the macrocycle
P. Khalili, C.B. Barnett, K.J. Naidoo. J. of Chemical Physics, 2013, 138, 184110 – 184117.Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association
K.J. Naidoo. Phys Chem Chem Phys. 2012, 14, 9026-9036.Molecular Details from Computational Reaction Dynamics for the Cellobiohydrolase I Glycosylation Reaction
C. B. Barnett, K. A. Wilkinson, and K. J. Naidoo. JACS. 2011. 133, 19474-19482.FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms
K. J. Naidoo. Science China. 2011.Acceleration of the GAMESS-UK electronic structure package on graphical processing units
K. A. Wilkinson, P. Sherwood, M. F. Guest, K. J. Naidoo. J. Comput. Chem. 2011, 32(10), 2313-2318.Using Solvent Binding and Dielectric Friction To Interpret the Hydration Behavior of Complex Anions
R. P. Matthews, G. A. Venter, K. J. Naidoo. J. Phys. Chem. B. 2011, 115 (5), 1045-1055.The Extent of Conformational Rigidity Determines Hydration in Nonaromatic Hexacyclic Systems
A. Boscaino, K. J. Naidoo. J. Phys. Chem. B. 2011,115 (11), 2608-2616.Computing Free Energy Hypersurfaces for Anisotropic Intermolecular Associations
J. Strumpfer, K. J. Naidoo. J. Comput. Chem. 2010, 31 (2), 308-316.Experimentally Consistent Ion Association Predicted for Metal Solutions from Free Energy Simulations
R. P. Matthews, K. J. Naidoo. J. Phys. Chem. B. 2010, 114 (21), 7286-7293.
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Biomarker Discovery:
Bioinformatics & Machine LearningGrowing Hierarchical Self-Organising Representation Map (GHSORM)
M. Coulson, C. Ferles, S. Winberg, K.J. Naidoo, Information Sciences, 2023, 642, 119121.BRIDGE: An open platform for reproducible protein-ligand simulations and free energy of binding calculations
T. Senapathi, C. B. Barnett, K.J. Naidoo, Bio-protocol, 2020, 10(17).Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
C. B. Barnett, T. Senapathi, K.J. Naidoo, Beilstein. Journal of Organic Chemistry, 2020, 16, 2540-2550.Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi, S. Bray, C. B. Barnett, B. Grüning, K. J. Naidoo. Bioinformatics, 2019.Denoising Autoencoder Self-Organizing Map (DASOM)
C. Ferles, Y. Papanikolaou, K.J. Naidoo. Journal of Neural Networks, 2018, 105, 112-131.The Glycome Analytics Platform: an integrative framework for glycobioinformatics
C.B. Barnett, K.F. Aoki-Kinoshita, K.J. Naidoo. Bioinformatics Journal, 2016, 32, 19, 3005-3011.Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes
J. Ashkani, K.J. Naidoo. Scientific Reports, 2016, 6.
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Drug Discovery:
Modelling & SynthesisModeling Reactions from Chemical Theories to Machine Learning
K.J. Naidoo, K.M. Merz, G.W. Wei, Journal of Chemical Information and Modeling, 2023, 63, 7273−7273.BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations
T. Senapathi, M. Suruzhon, C.B. Barnett, J.W. Essex, K. J. Naidoo. Journal of Chemical Information and Modeling. 2020ProtoCaller: Robust Automation of Binding Free Energy Calculations
M. Suruzhon, T. Senapathi, M.S. Bodnarchuk, R. Viner, I.D. Wall, C.B. Barnett, K.J. Naidoo, J.W. Essex. Journal of Chemical Information and Modeling. 2020, 60, 4, 1917–1921.Synthesis of (+)-Tacamonine via Stereoselective Radical Cyclization
Myles W. Smith, Jasmin Ferreira, Roger Hunter, Gerhard A. Venter, Hong Su. Organic Letters, 2019, 8740-8745Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants
Z.Qin, J.T. Munnoch, R. Devine, N.A. Holmes, R.F. Seipke, K.A. Wilkinson, B.Wilkinson and M.I. Hutchings. Chemical Science Journal , 2017, 8, 3218-3227.Conformational and electrostatic analysis of SN1 donor analogue glycomimetic inhibitors of ST3Gal-I mammalian sialyltransferase
W. Crous, K.J. Naidoo. Bioorganic & Medicinal Chemistry Journal, 2016, 24, 20, 4998-5005.Multidimensional Reaction Dynamics Reveal How the Enzyme TcTS Suppresses Competing Side Reactions and Their Side Products
I.L. Rogers, K.J. Naidoo. ACS Catalysis Journal, 2016, 6, 10, 6384-6392.Solution structures of chloroquine–ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy
D. Kuter, V. Streltsov, N. Davydova, G.A. Venter, K.J. Naidoo, T.J. Egan. Journal of Inorganic Biochemistry, 2016, 154, 114-125.Catalytic enantioselective acyl transfer: the case for 4-PPY with a C-3 carboxamide peptide auxiliary based on synthesis and modelling studies
R.E. Cozett, G.A. Venter, M.R. Gokada, and R. Hunter. Organic & Biomolecular Chemistry Journal, 2016, 14, 10914-10925.Profiling Transition-State Configurations on the Trypanosoma cruzitrans-Sialidase Free-Energy Reaction Surfaces
I. Rogers, K.J. Naidoo. Journal of Physical Chemistry B, 119, 2015 1192-1201.Computational Rationale for the Selective Inhibition of the Herpes Simplex Virus Type 1 Uracil-DNA Glycosylase Enzyme
U. Hendricks, W. Crous and K.J. Naidoo. Journal of Chem Information and Modeling, 54, 2014 3362-3372.Profiling transition-state configurations on the Trypanosoma cruzi trans-sialidase free-energy reaction surfaces
I.L. Rogers, K.J. Naidoo, Journal of Physical Chemistry B, 2014.Molecular Structures and Solvation of Free Monomeric and Dimeric Ferriheme in Aqueous Solution: Insights from Molecular Dynamics Simulations and Extended X-ray Absorption Fine Structure Spectroscopy
D. Kuter, V. Streltsov, N Davydova, G.A. Venter, K.J. Naidoo, T.J. Egan, Inorg. Chem., 2014.Conformational preferences of plumbagin with phenyl-1-thioglucoside conjugates in solution and bound to MshB determined by aromatic association
Ian L. Rogers, David W. Gammon, Kevin J. Naidoo, Carbohydrate Research, 2013, 371, 52-60.PNP Diminishes Guanosine Glycosidic Bond Strength Through Restrictive Ring Pucker as a Precursor to Phosphorylation
C.B. Barnett and K.J. Naidoo. J. Phys. Chem B., 2013, 117, 6019-6026.Hydration-determined orientational preferences in aromatic association from benzene dimer free energy volumes
M. R. Gamieldien, J. Strumpfer and K.J. Naidoo. J. Phys. Chem B. 2012, 116, 324-331.An enzyme-initiated Smiles rearrangement enables the development of an assay of MshB, the GlcNAc-Ins deacetylase of mycothiol biosynthesis
D.A. Lamprecht, N.O. Muneri, H. Eastwood, K.J. Naidoo, E. Strauss and A. Jardine. Organic & Biomolecular Chemistry. 2012, 10, 5878-5288.Experimental and Time-Dependent Density Functional Theory Characterization of the UV–Visible Spectra of Monomeric and μ-Oxo Dimeric Ferriprotoporphyrin IX
D. Kuter, G.A. Venter, K.J. Naidoo and T.J. Egan. Inorganic Chemistry. 2012, 51, 10233-10250.Conformational preferences in diglycosyl disulfides: NMR and molecular modeling studies
K Feher, R.P Matthews, K.E. Kover, K.J. Naidoo, L. Szilagyi. Carbohydrate Research. 2011, 346 2612-2621.Optimal Configurations of "Capped" beta-Cyclodextrin Dimers in Water Maximise Hydrophobic Association
M. R. Gamieldien, I. Maestre, C. Jaime, K. J. Naidoo. Chem. Phys. Chem. 2010, 11 (2), 452-459.Pyranose Ring Transition State Is Derived from Cellobiohydrolase I Induced Conformational Stability and Glycosidic Bond Polarization
C. B. Barnett, K. Wilkinson, K. J. Naidoo. J. Am. Chem. Soc. 2010, 132 (37), 12800–12803.Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations
C. B. Barnett, K. J. Naidoo. J. Phys. Chem. B. 2010, 114 (51), 17142-17154.Free Energies from Adaptive Reaction Coordinate Forces (FEARCF): an application to ring puckering
C. B. Barnett, K. J. Naidoo. Mol. Phys. 2009, 107, 1243–1250.Calculating Ring Pucker Free Energy Surfaces from Reaction Coordinate Forces
C. B. Barnett, K. J. Naidoo, AIP Conference Proceedings. 2009, 1102, 214Conformational flexibility of sulphur linked saccharides a possible key to their glycosidase inhibitor activity
G. A. Venter, R. P. Matthews, K. J. Naidoo. Molecular Simulation. 2008, 34 (4), 391-401.Glucose Orientation and Dynamics in α-, β-, and γ-Cyclodextrins
K. J. Naidoo, M. R. Gamieldien, J. Y.-J. Chen, G. Widmalm, A. Maliniak. J. Phys. Chem. B. 2008, 112, 15151–15157.Stereoelectronic and Solvation Effects Determine Hydroxymethyl Conformational Preferences in Monosaccharides
C. B. Barnett, K. J. Naidoo. J. Phys. Chem. B. 2008, 112, 15450–15459.
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Chemical Models and Assays
Universal Glycosyltransferase Continuous Assay for Uniform Kinetics and Inhibition Database Development and Mechanistic Studies Illustrated on ST3GAL1, C1GALT1, and FUT1
Abdullateef Nashed and Kevin J. Naidoo, ACS Omega, 2024, 9, 15, 17518–17532.Molecular dynamics simulations of the structural properties and electrical conductivities of CaO–MgO–Al2O3–SiO2 melts
L. Mongalo, A.S. Lopis, G.A. Venter. Journal of Non-Crystalline Solids, 2016, 452, 194-202.Water-Soluble Half-Sandwich RuII–Arene Complexes: Synthesis, Structure, Electrochemistry, DFT Studies, and Aqueous Phase Hydroformylation of 1-Octene
Leah C. Matsinha, Peter Malatji, Alan T. Hutton, Gerhard A. Venter, Selwyn F. Mapolie and Gregory S. Smith, European Journal of Inorganic Chemistry, 2013, 4318-4328.Structural and DFT Studies on the Polymorphism of a Cadmium(II) Dipicolinate Coordination Polymer
Boris-Marko Kukovec, Gerhard A. Venter and Clive L. Oliver. Crystal Growth & Design. 2011. 12, 456-465.