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Showing 1 to 6 of 6 for “"free energy methods"”.
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Efficient Methods for Exploring Chemical Space in Computational Drug Discovery
In this work novel computational methods will be developed to efficiently explore chemical space in the search for compounds with desirable properties. To improve the efficiency of exploration two methods will be used: reducing the cost of evaluating a point in chemical space, or reducing the …
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A Highly Charged Topic: Intrinsically Disordered Proteins and Protein pKa Values
… how MD simulations alongside non-equilibrium free energy methods and theory could be used to compute coupled and uncoupled pKa values for more than 140 amino acid residues spanning 13 proteins. We achieved performance that matched or exceeded several state-of-the-art alternative approaches.
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A comparative study between the cubic spline and b-spline interpolation methods in free energy calculations
Numerical methods are essential in computational science, as analytic calculations for large datasets are impractical. Using numerical methods, one can approximate the problem to solve it with basic arithmetic operations. Interpolation is a commonly-used method, inter alia, constructing the value …
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Phase behaviour of multicomponent systems from computer simulations
… used to make accurate predictions. Here, we use free-energy methods and thermodynamic integration to characterise the liquidus line of the eutectic phase diagram of a mixture of choline chloride and urea, in order to better understand what governs the behaviour of deep eutectic solvents and how …
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Molecular Simulation of Mutation Effects on Protein Folding and Function
… stability, we developed an MSM-based hydrophobic free energy of transfer (HT) model to estimate mutation effects. Our HT model results agree better with experiment than other state-of-the-art computational methods. Chapter two describes how we have used approximately 43000 relative binding free …