Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations. - Kevin J. Naidoo; Michelle Kuttel (J. Comput. Chem., 2001)

Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations. - Michelle Kuttel; John W. Brady; Kevin J. Naidoo (J. Comput. Chem., 2002)

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. - Ramkumar Rajamani; Kevin J. Naidoo; Jiali Gao (J. Comput. Chem., 2003)

Computing free energy hypersurfaces for anisotropic intermolecular associations. - Johan Strümpfer; Kevin J. Naidoo (J. Comput. Chem., 2010)

Acceleration of the GAMESS-UK electronic structure package on graphical processing units. - Karl A. Wilkinson; Paul Sherwood; Martyn F. Guest; Kevin J. Naidoo (J. Comput. Chem., 2011)

Computational Rationale for the Selective Inhibition of the Herpes Simplex Virus Type 1 Uracil-DNA Glycosylase Enzyme. - Umraan Hendricks; Werner Crous; Kevin J. Naidoo (J. Chem. Inf. Model., 2014)

Quantum supercharger library: Hyper-parallelism of the Hartree-Fock method. - Kyle D. Fernandes; C. Alicia Renison; Kevin J. Naidoo (J. Comput. Chem., 2015)

Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics. - C. Alicia Renison; Kyle D. Fernandes; Kevin J. Naidoo (J. Comput. Chem., 2015)

The Glycome Analytics Platform: an integrative framework for glycobioinformatics. - Christopher B. Barnett; Kiyoko F. Aoki-Kinoshita; Kevin J. Naidoo (Bioinform., 2016)

Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction. - Ian L. Rogers; Kevin J. Naidoo (J. Comput. Chem., 2017)

Denoising Autoencoder Self-Organizing Map (DASOM). - Christos Ferles; Yannis Papanikolaou; Kevin J. Naidoo (Neural Networks, 2018)

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). - Tharindu Senapathi; Simon Bray; Christopher B. Barnett; Björn A. Grüning; Kevin J. Naidoo (Bioinform., 2019)

BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations. - Tharindu Senapathi; Miroslav Suruzhon; Christopher B. Barnett; Jonathan W. Essex; Kevin J. Naidoo (J. Chem. Inf. Model., 2020)

ProtoCaller: Robust Automation of Binding Free Energy Calculations. - Miroslav Suruzhon; Tharindu Senapathi; Michael S. Bodnarchuk; Russell C. Viner; Ian D. Wall; Christopher B. Barnett; Kevin J. Naidoo; Jonathan W. Essex (J. Chem. Inf. Model., 2020)

Anisotropic numerical potentials for coarse-grained modeling from high-speed multidimensional lookup table and interpolation algorithms. - Ananya Gangopadhyay; Simon Winberg; Kevin J. Naidoo (J. Comput. Chem., 2021)

Molecular mechanisms from reaction coordinate graph enabled multidimensional free energies illustrated on water dimer hydrogen bonding. - Tomás Bruce-Chwatt; Kevin J. Naidoo (J. Comput. Chem., 2022)

Growing Hierarchical Self-Organising Representation Map (GHSORM). - Matthew Coulson; Christos Ferles; Simon Winberg; Kevin J. Naidoo (Inf. Sci., 2023)

Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. - Thereza A. Soares; Zoe Cournia; Kevin J. Naidoo; Rommie E. Amaro; Habibah A. Wahab; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform. - Hikmet Emre Kaya; Kevin J. Naidoo (Bioinform., 2023)

Modeling Reactions from Chemical Theories to Machine Learning. - Kevin J. Naidoo; Kenneth M. Merz Jr.; Guo-Wei Wei 001 (J. Chem. Inf. Model., 2023)