Christopher Barnett University of Cape Town
1 protocol


Kevin J. Naidoo
  • Faculty, University of Cape Town
Research focus
  • Biophysics
  • Scientific Computing Methods development for Biomedical Applications
    Free Energy Method Development
    Reaction Dynamics of Glycoenzymes
    Machine Learning for Cancer Gene Expression Data sets
    Rational Design of Diagnostics and Therapeutics for Cancer
  • 1 Author merit

Education

PhD, University of Michigan, 1993

Lab information

Kevin J Naidoo Lab
http://www.scientificomputing.uct.ac.za/

Publications

SELECTED CANCER GENE EXPRESSION DIAGNOSTIC RELATED PAPERS
Ferles, C., Papanikolaou, Y. & Naidoo, K. J. Denoising Autoencoder Self-Organizing Map (DASOM). Neural Networks 105, 112-131, doi:https://doi.org/10.1016/j.neunet.2018.04.016 (2018).

Ferles, C., Papanikolaou, Y. & Naidoo, K. J. Cancer Types: RNA Sequencing Values from Tumor Samples/Tissues May 2018
DOI: 10.17632/sf5n64hydt.1

Ashkani, J. & Naidoo, K. J. Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes. Scientific Reports 6, 26451, doi:10.1038/srep26451 (2016).


SELECTED BIOINFORMATICS PAPERS
Suruzhon, M., Senapathi, T., Bodnarchuk, M. S., Viner, R., Wall, I. D., Barnett, C. B., Naidoo, K. J. & Essex, J. W. ProtoCaller: Robust Automation of Binding Free Energy Calculations. Journal of Chemical Information and Modeling 60, 1917-1921, doi:10.1021/acs.jcim.9b01158 (2020).

Senapathi, T., Bray, S., Barnett, C. B., Gruning, B. & Naidoo, K. J. Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinformatics 35, 3508-3509, doi:10.1093/bioinformatics/btz107 (2019).

Barnett, C. B., Aoki-Kinoshita, K. F. & Naidoo, K. J. The Glycome Analytics Platform: an integrative framework for glycobioinformatics. Bioinformatics 32, 3005-3011, doi:10.1093/bioinformatics/btw341 (2016).

SELECTED REACTION DYNAMICS PAPERS
Rogers, I. L. & Naidoo, K. J. Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction.
J Comput Chem 38, 1789-1798, doi:10.1002/jcc.24820 (2017).

Rogers, I. L. & Naidoo, K. J. Multidimensional Reaction Dynamics Reveal How the Enzyme TcTS Suppresses Competing Side Reactions and Their Side Products. ACS Catalysis, 6384-6392, doi:10.1021/acscatal.6b01522 (2016).

Govender, K., Gao, J. & Naidoo, K. J. AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems. Journal of Chemical Theory and Computation 10, 4694-4707, doi:10.1021/ct500372s (2014).

Renison, C. A., Fernandes, K. D. & Naidoo, K. J. Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initioQM/MM dynamics. J. Comp. Chem. 36, 1410-1419, doi:10.1002/jcc.23938 (2015).

Crous, W., Field, M. J. & Naidoo, K. J. Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary. Journal of Chemical Theory and Computation 10, 1727-1738, doi:10.1021/ct400903n (2014).
1 Protocol published
BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 806, Q&A: 0
Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein ...
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