FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY write by Peng He. This book was released on 2018. FREE ENERGY SIMULATIONS AND STRUCTURAL STUDIES OF PROTEIN-LIGAND BINDING AND ALLOSTERY available in PDF, EPUB and Kindle. Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics.
Understanding Protein Dynamics, Binding and Allostery for Drug Design
Understanding Protein Dynamics, Binding and Allostery for Drug Design - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Understanding Protein Dynamics, Binding and Allostery for Drug Design write by Guang Hu. This book was released on 2021-06-08. Understanding Protein Dynamics, Binding and Allostery for Drug Design available in PDF, EPUB and Kindle.
Protein-Ligand Interactions
Protein-Ligand Interactions - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Protein-Ligand Interactions write by Holger Gohlke. This book was released on 2012-05-21. Protein-Ligand Interactions available in PDF, EPUB and Kindle. Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Computational Methods for Estimating the Kinetic Parameters of Biological Systems
Computational Methods for Estimating the Kinetic Parameters of Biological Systems - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Computational Methods for Estimating the Kinetic Parameters of Biological Systems write by Quentin Vanhaelen. This book was released on 2022-12-24. Computational Methods for Estimating the Kinetic Parameters of Biological Systems available in PDF, EPUB and Kindle. This detailed book provides an overview of various classes of computational techniques, including machine learning techniques, commonly used for evaluating 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), and the prediction of relatively large set of kinetic rates of reactions usually found in quantitative models of large biological networks. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that leads to successful results. Authoritative and practical, Computational Methods for Estimating the Kinetic Parameters of Biological Systems will be of great interest for researchers working through the challenge of identifying the best type of algorithm and who would like to use or develop a computational method for the estimation of kinetic parameters.
Protein–Ligand Binding Thermodynamics
Protein–Ligand Binding Thermodynamics - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Protein–Ligand Binding Thermodynamics write by Justin M. Miller. This book was released on 2023-06-01. Protein–Ligand Binding Thermodynamics available in PDF, EPUB and Kindle. Ligand binding by macromolecules represents a core event of broad relevance to a range of systems, including catalytic systems alongside noncatalytic systems such as nucleic acid binding by transcription factors or extracellular ligand binding by proteins involved in signaling pathways. The scope of this primer is constrained to introduce only foundational models without significant discussion of more advanced topics such as allosteric or linkage effects. Linkage occurs when the binding of a ligand is influenced by the binding of another molecule of the same ligand (homotropic linkage), the binding of a different ligand (heterotropic linkage), physical variables such as temperature or pressure (physical linkage), or changes in macromolecular assembly state (polysteric linkage). Taking this into account, the foundational themes presented in this primer can be used to describe any macromolecule–ligand interaction either by direct use of the models and techniques described here or by applying them to develop more advanced models to explain additional complexities such as those allosteric or linkage effects just mentioned. The target audience of this primer is the senior undergraduate or junior graduate student who lacks a foundation in ligand-binding thermodynamics. As such, we have focused primarily on foundational thermodynamic treatments and presented only general discussions of relevant experimental designs. Readers of this primer will learn how to build a working understanding of common factors that promote energetic favorability for ligand binding; develop a functional toolbox to understand ligand binding from the perspective of collecting, plotting, and interpreting ligand-binding data; enhance proficiency in deriving thermodynamic mechanisms for ligand binding; and become comfortable in interpreting binding data reported in the literature and independently expanding knowledge beyond the scope introduced in this primer.
