Daria B. Kokh

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We present TRAPP (TRAnsient Pockets in Proteins), a new automated software platform for tracking, analysis, and visualization of binding pocket variations along a protein motion trajectory or within an ensemble of protein structures that may encompass conformational changes ranging from local side chain fluctuations to global backbone motions. TRAPP(More)
The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein-protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes,(More)
Localized molecular orbitals (LMOs) derived from exchange maximization with respect to all atom-centered basis functions in the basis set are shown to generate a good starting electronic field for self-consistent field calculations on extended systems such as metal clusters, for which well-defined chemical bonds are not present. Examples studied are a(More)
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