Software
The Scientific Computing Research Unit develops high-performance simulation software as well as chemical and chemical biology modelling
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BRIDGE
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
T. Senapathi, S. Bray, C. B. Barnett, B. Grüning, K. J. Naidoo. Bioinformatics, 2019. -
SLASH
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. -
FEARCF
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, 1802-1813Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association
K.J. Naidoo. Phys Chem Chem Phys. 2012, 14, 9026-9036. -
QSL
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. -
DASOM
Denoising Autoencoder Self-Organizing Map (DASOM)
C. Ferles, Y. Papanikolaou, K.J. Naidoo. Journal of Neural Networks, 2018, 105, 112-131.