Titlebook: Computational Methods for Estimating the Kinetic Parameters of Biological Systems; Quentin Vanhaelen Book 2022 Springer Science+Business M

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The Role of Ligand Rebinding and Facilitated Dissociation on the Characterization of Dissociation R sites, and lies at the backbone of pharmaceutical, biosensing, and biomolecular research. The extraction of dissociation rates from SPR-response signals often relies on several commonly adopted assumptions, one of which is the exponential decay of the dissociation part of the response signal. Howev

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Umbrella Sampling-Based Method to Compute Ligand-Binding Affinity,rms. The binding/unbinding pathways of these protein–inhibitor complexes can be rather straightforwardly sampled by using umbrella sampling (US) simulation methods. During a US simulation, the . atoms of the protein are restrained via a harmonic force. The potential of mean force (PMF) along the bin

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Creating Maps of the Ligand Binding Landscape for Kinetics-Based Drug Discovery,can be used to get information about ligand binding transition states, which form the rate-limiting step of the binding and release processes. However, these simulations are typically limited by the presence of large energy barriers that separate stable poses of interest. Here we describe a simulati

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,Prediction of Protein–Protein Binding Affinities from Unbound Protein Structures,eractions between proteins that are both time and location specific. The strength, or binding affinity, of protein–protein interactions ranges between the micro- and the nanomolar association constant, often dictating the molecular mechanisms underlying the interaction and the longevity of the compl

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Parameter Optimization for Ion Channel Models: Integrating New Data with Known Channel Properties,ng kinetics is not trivial when the mechanism is complex, and a large number of parameters must be extracted from data. Furthermore, the information contained in the data is often limited, and the model may not be fully determined. The solution is to reduce the number of parameters and to estimate t

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Book 2022ating kinetic parameters of biological systems. Focusing on three distinct situations, the volume covers the prediction of the kinetics of enzymatic reactions, the prediction of the kinetics of protein-protein or protein-ligand interactions (binding rates, dissociation rates, binding affinities), an