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List of works by Kevin J. Naidoo

AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems

scientific article published on January 2014

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

scientific article published on 3 May 2011

An enzyme-initiated Smiles rearrangement enables the development of an assay of MshB, the GlcNAc-Ins deacetylase of mycothiol biosynthesis

scientific article published on 7 June 2012

Anisotropic numerical potentials for coarse‐grained modeling from high‐speed multidimensional lookup table and interpolation algorithms

scientific article published on 08 February 2021

C-2-aryl O-substituted HI-236 derivatives as non-nucleoside HIV-1 reverse-transcriptase inhibitors

scientific article

Carbohydrate solution simulations: producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

scientific article

Computational rationale for the selective inhibition of the herpes simplex virus type 1 uracil-DNA glycosylase enzyme

scientific article

Conformational preferences in diglycosyl disulfides: NMR and molecular modeling studies

scientific article published on 23 July 2011

Conformational preferences of plumbagin with phenyl-1-thioglucoside conjugates in solution and bound to MshB determined by aromatic association

scientific article

Contact ion pair between Na+ and PtCl(6)(2-) favored in methanol

scientific article published in November 2003

Evaluating AM1/d-CB1 for Chemical Glycobiology QM/MM Simulations

scientific article published in October 2014

Experimental and time-dependent density functional theory characterization of the UV-visible spectra of monomeric and μ-oxo dimeric ferriprotoporphyrin IX.

scientific article published on 10 September 2012

Experimentally consistent ion association predicted for metal solutions from free energy simulations

scientific article published on June 2010

Free energy surfaces for the alpha(1 --> 4)-glycosidic linkage: implications for polysaccharide solution structure and dynamics

scientific article published in April 2005

Geometric hydration shells for anionic platinum group metal chloro complexes

scientific article published in April 2002

Glucose orientation and dynamics in alpha-, beta-, and gamma-cyclodextrins

scientific article published in November 2008

Glycosidic Linkage Rotations Determine Amylose Stretching Mechanism

scientific article published on 01 January 2005

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes

scientific article published on 20 May 2016

Haemozoin (beta-haematin) biomineralization occurs by self-assembly near the lipid/water interface

scientific article published in September 2006

Hydration-determined orientational preferences in aromatic association from benzene dimer free energy volumes

scientific article published on 13 December 2011

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution

scientific article published on November 2003

Interpreting medium ring canonical conformers by a triangular plane tessellation of the macrocycle.

scientific article published in May 2013

Modeling Platinum Group Metal Complexes in Aqueous Solution

scientific article published on 01 May 2001

Molecular details from computational reaction dynamics for the cellobiohydrolase I glycosylation reaction

scientific article published on 9 November 2011

Molecular dynamics simulations of the N-linked oligosaccharide of the lectin from Erythrina corallodendron ⬇️

scientific article published on November 1, 1997

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

scientific article published on 2 October 2014

Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association

scientific article published on 29 May 2012

NMR studies of molecular conformations in alpha-cyclodextrin.

scientific article published on 25 June 2008

Optimal configurations of "capped" beta-cyclodextrin dimers in water maximise hydrophobic association

scientific article

PNP diminishes guanosine glycosidic bond strength through restrictive ring pucker as a precursor to phosphorylation.

scientific article published on 10 May 2013

Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction

scientific article

Profiling transition-state configurations on the Trypanosoma cruzi trans-sialidase free-energy reaction surfaces

scientific article published on 24 September 2014

ProtoCaller: Robust Automation of Binding Free Energy Calculations

scientific article published on 26 March 2020

Pyranose ring transition state is derived from cellobiohydrolase I induced conformational stability and glycosidic bond polarization

scientific article

Quantum supercharger library: hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics

scientific article published on 14 May 2015

Quantum supercharger library: hyper-parallelism of the Hartree-Fock method

scientific article published on 14 May 2015

Ramachandran free-energy surfaces for disaccharides: trehalose, a case study

scientific article

Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations

scientific article published on 7 December 2010

Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary

scientific article published on 01 April 2014

Solution structures of chloroquine-ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy

scientific article published on 11 June 2015

Stereoelectronic and solvation effects determine hydroxymethyl conformational preferences in monosaccharides

scientific article

The extent of conformational rigidity determines hydration in nonaromatic hexacyclic systems

scientific article

Using Solvent Binding and Dielectric Friction To Interpret the Hydration Behavior of Complex Anions ⬇️

scientific article published on January 20, 2011

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