Free Energy Methods Involving Quantum Physics, Path Integrals, and Virtual Screenings PDF Download
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Author: Christoph Gorgulla
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: Christoph Gorgulla
Publisher:
ISBN:
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Languages : en
Pages :
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Author: Vasanthanathan Poongavanam
Publisher: John Wiley & Sons
ISBN: 3527840737
Category : Science
Languages : en
Pages : 882
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Computational Drug Discovery A comprehensive resource that explains a wide array of computational technologies and methods driving innovation in drug discovery Computational Drug Discovery: Methods and Applications (2 volume set) covers a wide range of cutting-edge computational technologies and computational chemistry methods that are transforming drug discovery. The book delves into recent advances, particularly focusing on artificial intelligence (AI) and its application for protein structure prediction, AI-enabled virtual screening, and generative modeling for compound design. Additionally, it covers key technological advancements in computing such as quantum and cloud computing that are driving innovations in drug discovery. Furthermore, dedicated chapters that addresses the recent trends in the field of computer aided drug design, including ultra-large-scale virtual screening for hit identification, computational strategies for designing new therapeutic modalities like PROTACs and covalent inhibitors that target residues beyond cysteine are also presented. To offer the most up-to-date information on computational methods utilized in computational drug discovery, it covers chapters highlighting the use of molecular dynamics and other related methods, application of QM and QM/MM methods in computational drug design, and techniques for navigating and visualizing the chemical space, as well as leveraging big data to drive drug discovery efforts. The book is thoughtfully organized into eight thematic sections, each focusing on a specific computational method or technology applied to drug discovery. Authored by renowned experts from academia, pharmaceutical industry, and major drug discovery software providers, it offers an overview of the latest advances in computational drug discovery. Key topics covered in the book include: Application of molecular dynamics simulations and related approaches in drug discovery The application of QM, hybrid approaches such as QM/MM, and fragment molecular orbital framework for understanding protein-ligand interactions Adoption of artificial intelligence in pre-clinical drug discovery, encompassing protein structure prediction, generative modeling for de novo design, and virtual screening. Techniques for navigating and visualizing the chemical space, along with harnessing big data to drive drug discovery efforts. Methods for performing ultra-large-scale virtual screening for hit identification. Computational strategies for designing new therapeutic models, including PROTACs and molecular glues. In silico ADMET approaches for predicting a variety of pharmacokinetic and physicochemical endpoints. The role of computing technologies like quantum computing and cloud computing in accelerating drug discovery This book will provide readers an overview of the latest advancements in computational drug discovery and serve as a valuable resource for professionals engaged in drug discovery.
Author: Kira A. Armacost
Publisher:
ISBN: 9780841298057
Category : Drug development
Languages : en
Pages :
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"This book is about Free Energy Methods in Drug Discovery: Current State and Future Directions"--
Author: Kevin Bishop
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Free energy calculations are one of the most powerful tools within modern theoretical chemistry and are often used to make comparisons with experimental results. Existing free energy calculations are typically performed for classical molecular dynamics simulations but there are certain systems where nuclear quantum effects play an integral role. Specifically, systems with light atoms or low temperatures are the most influenced by such nuclear quantum effects and the development of Feynman path integrals [1] has been effective in accurately describing the quantum nature of these nuclei [2-8]. The primary objective of this thesis is the development of a pair of methodologies to calculate free energies utilizing path integral molecular dynamics to account for nuclear quantum effects. Prior to the development of these free energy methodologies, this thesis presents a communication interface between the OpenMM and MMTK software packages that has been previously published [9]. This interface allows for users of MMTK to take advantage of the performance of OpenMM without major modifications to existing simulation scripts. Notably, the serial OpenMM integrator is shown to provide a 3x performance gain in comparison to a standard MMTK simulation while the GPU implementations of OpenMM provide over a 400x performance gain for larger systems with periodic boundary conditions. The first path integral free energy methodology of this thesis combines the existing um- brella sampling technique [10,11] with path integral molecular dynamics. This methodology has been previously published and proposes that the umbrella sampling biasing potential only needs to be applied to a single path integral bead [12]. Furthermore, this proposed methodology is successfully benchmarked for a pair of Lennard-Jones dimer systems before being applied to the more difficult water dimer. The free energy profiles obtained from simulation are then used to calculate a free energy difference of -12.90 ± 0.05 kJ/mol for the MB-Pol potential in comparison to the experimental dissociation energy of -13.2 ± 0.12 kJ/mol [13]. The second path integral free energy methodology introduces a constraint within the path integral molecular dynamics simulations as opposed to an umbrella sampling restraint. Specifically, this methodology applies a constraint to an individual path integral bead in a manner that is similar to the concept of thermodynamic integration for classical simulations [14]. Formal estimators for the derivative of the free energy have been developed by Iouchtchenko et al. [15] and the results presented in this thesis analyze the effectiveness of these estimators for molecular dynamics simulations of Lennard-Jones and water dimers. Additionally, a new estimator is developed and the resulting free energy profiles are used to evaluate a free energy difference for the water dimer of -13.03 ± 0.14 kJ/mol, which is within the errors of the experimental dissociation energy [13]. Overall, this thesis provides a theoretical framework to study the free energy of weakly bound systems over a broad range of temperatures. It is important to note that these methodologies were insufficient below 25 K and it remains more practical to use reaction coordinates that are not distances at such temperatures. Nevertheless, the extension and application of these methodologies to more complicated systems remains an area of exciting development.
Author: Volker Bach
Publisher: Springer
ISBN: 3319063790
Category : Science
Languages : en
Pages : 410
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This book provides a broad description of the development and (computational) application of many-electron approaches from a multidisciplinary perspective. In the context of studying many-electron systems Computer Science, Chemistry, Mathematics and Physics are all intimately interconnected. However, beyond a handful of communities working at the interface between these disciplines, there is still a marked separation of subjects. This book seeks to offer a common platform for possible exchanges between the various fields and to introduce the reader to perspectives for potential further developments across the disciplines. The rapid advances of modern technology will inevitably require substantial improvements in the approaches currently used, which will in turn make exchanges between disciplines indispensable. In essence this book is one of the very first attempts at an interdisciplinary approach to the many-electron problem.
Author: R. P. Feynman
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: Alexander Altland
Publisher: Cambridge University Press
ISBN: 0521769752
Category : Science
Languages : en
Pages : 785
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This primer is aimed at elevating graduate students of condensed matter theory to a level where they can engage in independent research. Topics covered include second quantisation, path and functional field integration, mean-field theory and collective phenomena.
Author: Christophe Chipot
Publisher: Springer Science & Business Media
ISBN: 3540384472
Category : Language Arts & Disciplines
Languages : en
Pages : 528
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Book Description
Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.
Author: Luiz C. L. Botelho
Publisher:
ISBN: 9781607419082
Category : Mathematics
Languages : en
Pages : 336
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Author: Michael Bachmann
Publisher:
ISBN:
Category :
Languages : en
Pages : 209
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