Simulation Based Free Energy Calculations And Drug Design PDF Download
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Author | : M. Rami Reddy |
Publisher | : Springer Science & Business Media |
Total Pages | : 420 |
Release | : 2001-12-31 |
Genre | : Medical |
ISBN | : 9780306466762 |
Download Free Energy Calculations in Rational Drug Design Book in PDF, ePub and Kindle
Free energy calculations represent the most accurate computational method available for predicting enzyme inhibitor binding affinities. Advances in computer power in the 1990s enabled the practical application of these calculations in rationale drug design. This book represents the first comprehensive review of this growing area of research and covers the basic theory underlying the method, numerous state of the art strategies designed to improve throughput and dozen examples wherein free energy calculations were used to design and evaluate potential drug candidates.
Author | : Randall J. Radmer |
Publisher | : |
Total Pages | : 316 |
Release | : 1996 |
Genre | : Drugs |
ISBN | : |
Download Simulation Based Free Energy Calculations and Drug Design Book in PDF, ePub and Kindle
Author | : Christophe Chipot |
Publisher | : Springer Science & Business Media |
Total Pages | : 528 |
Release | : 2007-01-08 |
Genre | : Language Arts & Disciplines |
ISBN | : 3540384472 |
Download Free Energy Calculations Book in PDF, ePub and Kindle
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 | : Kira A. Armacost |
Publisher | : |
Total Pages | : |
Release | : 2021 |
Genre | : Drug development |
ISBN | : 9780841298057 |
Download Free Energy Methods in Drug Discovery Book in PDF, ePub and Kindle
"This book is about Free Energy Methods in Drug Discovery: Current State and Future Directions"--
Author | : Kenneth M. Merz |
Publisher | : Cambridge University Press |
Total Pages | : 289 |
Release | : 2010-05-31 |
Genre | : Medical |
ISBN | : 0521887232 |
Download Drug Design Book in PDF, ePub and Kindle
This book provides a complete snapshot of various experimental approaches to structure-based and ligand-based drug design and is illustrated with more than 200 images.
Author | : Francesco L. Gervasio |
Publisher | : John Wiley & Sons |
Total Pages | : 420 |
Release | : 2019-01-04 |
Genre | : Medical |
ISBN | : 3527806857 |
Download Biomolecular Simulations in Structure-Based Drug Discovery Book in PDF, ePub and Kindle
A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.
Author | : Sergio Decherchi |
Publisher | : Frontiers Media SA |
Total Pages | : 119 |
Release | : 2021-06-08 |
Genre | : Science |
ISBN | : 2889668630 |
Download Molecular Dynamics and Machine Learning in Drug Discovery Book in PDF, ePub and Kindle
Dr. Sergio Decherchi and Dr. Andrea Cavalli are co-founders of BiKi Technologies s.r.l. - a company that commercializes a Molecular Dynamics-based software suite for drug discovery. All other Topic Editors declare no competing interests with regards to the Research Topic subject.
Author | : Matthew Hurley |
Publisher | : |
Total Pages | : 0 |
Release | : 2022 |
Genre | : |
ISBN | : |
Download Advancing Simulation Methods for Molecular Design and Drug Discovery Book in PDF, ePub and Kindle
Investigating interactions between proteins and small molecules at an atomic scale is fundamental towards understanding biological processes and designing novel candidates during the pre-clinical stages of drug discovery. By optimizing the methods used to study these interactions in terms of accuracy and computational cost, we can accelerate this aspect of biological research and contribute more readily to therapeutic design. While biological assays and other experimental techniques are invaluable in quantitatively determining in vitro and in vivo inhibition activity, as well as validating computational predictions, there is an inherent benefit in the possible throughput provided by molecular dynamics (MD) simulations and related computational methods. These calculations provide researchers with unparalleled access to large amounts of all-atom sampling of biological systems, including non-physical pathways and other enhanced sampling methods. This dissertation presents research into advancing the application of expanded ensemble and other simulation-based methods of ligand design towards reliable and efficient absolute free energy of binding calculations on the scale of hundreds to thousands of small molecule ligands. This culminates in a combined workflow that allows for an automated approach to the force-field parameterization of custom systems, simulation preparation, optimization of the restraint and sampling protocols, production free energy simulations, and analysis that has facilitated the computation of absolute binding free energy predictions. Specifically highlighted is our ongoing effort to discover novel inhibitors of the main protease (Mpro) of SARS-CoV-2 as well as participation in the SAMPL9 Host-Guest Challenge.
Author | : Pooja A. Chawla |
Publisher | : Walter de Gruyter GmbH & Co KG |
Total Pages | : 543 |
Release | : 2024-10-07 |
Genre | : Science |
ISBN | : 3111207595 |
Download Computational Drug Discovery Book in PDF, ePub and Kindle
Computational methods and understanding computational models are important in modern drug discovery. The book focuses on computational approaches that can improve the development of in silico methodologies. It includes lead hit methods, docking algorithms, computational chiral compounds, structure-based drug design, GROMACS and NAMD, structural genomics, toxicity prediction, enzyme inhibitors and peptidomimetic therapeutics
Author | : Pavel Klimovich |
Publisher | : |
Total Pages | : 124 |
Release | : 2015 |
Genre | : |
ISBN | : 9781321964455 |
Download Testing, Understanding, and Automating Applications of Alchemical Free Energy Calculations Book in PDF, ePub and Kindle
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. Currently, the most important challenges in this field are primarily in two areas. One is a direct corollary of the finite simulation length and involves problems of obtaining reliable free energy estimates when sampling is inadequate. The other one can be classified as a logistical challenge--that of obtaining the desired results via as automated a process as possible. This includes such problems as planning of free energy calculations, and their set up and analysis. Here, I present several studies in which I address these challenges. Chapter 1 focuses on the importance of accounting for ligand binding mode interconversions in relative binding free energy calculations, emphasizing lengthening simulations does not simply eliminate all sampling problem. In Chapter 2--a description of the work done as a result of participating in the SAMPL09 contest--we show that within a given force field framework the conformational changes of even small, drug-like, molecules can be quite slow, forcing us to employ biased sampling techniques to obtain correct transfer free energies. In addition, the work helped reveal deficiencies of current force fields in the description of hydroxyl-containing molecules. An attempt to address logistical challenges resulted in the creating of two pieces of software. Chapter 3 describes a tool that automates setup of relative free energy calculations. Chapter 4 reviews best practices for analysis of alchemical free energy calculations and introduces alchemical-analysis.py, a freely available software that implements the analysis practices for several simulation packages and features a variety of innovative statistical and graphical ways of assessing the quality of the analyzed data.