Michelle Kuttel

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We present a CHARMM Carbohydrate Solution Force Field (CSFF) suitable for nanosecond molecular dynamics computer simulations. The force field was derived from a recently published sugar parameter set.1 Dihedral angle parameters for the primary alcohol as well as the secondary hydroxyl groups were adjusted. Free energy profiles of the hydroxymethyl group for(More)
We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress(More)
We report a hybrid parallel central and graphics processing units (CPU-GPU) implementation of a coarse-grained model for replica exchange Monte Carlo (REMC) simulations of protein assemblies. We describe the design, optimization, validation, and benchmarking of our algorithms, particularly the parallelization strategy, which is specific to the requirements(More)
Standard molecular visualizations, such as the classic ball-and-stick model, are not suitable for large, complex molecules because the overall molecular structure is obscured by the atomic detail. For proteins, the more abstract ribbon and cartoon representations are instead used to reveal large scale molecular conformation and connectivity. However, there(More)
—CarbBuilder is a software tool for building 3D structures of carbohydrates, which are the most structurally varied of all molecular classes. CarbBuilder was designed with the dual aims of portability and adaptability, using an iterative software development approach. CarbBuilder employs a simple algorithm, using heuristics based upon experimental data to(More)
In this work, a model for the interaction between CYP2B4 and the FMN domain of rat P450-oxidoreductase is built using as template the structure of a bacterial redox complex. Amino acid residues identified in the literature as cytochrome P450 (CYP)-redox partner interfacial residues map to the interface in our model. Our model supports the view that the(More)
Many South Africans are functionally illiterate, which impacts adversely on their further education and job prospects. As literacy deficits begin in primary school, it is vitally important to improve reading engagement in children aged 6 to 13 years. In this study, we explored the use of mobile applications to improve children's engagement with, and(More)