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Virtual Screening in Drug Discovery

Virtual Screening in Drug Discovery
Author: Juan Alvarez
Publisher: CRC Press
Total Pages: 498
Release: 2005-03-24
Genre: Medical
ISBN: 1420028774

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Virtual screening can reduce costs and increase hit rates for lead discovery by eliminating the need for robotics, reagent acquisition or production, and compound storage facilities. The increased robustness of computational algorithms and scoring functions, the availability of affordable computational power, and the potential for timely structural


Virtual Screening and Drug Docking

Virtual Screening and Drug Docking
Author:
Publisher: Academic Press
Total Pages: 266
Release: 2022-11-23
Genre: Science
ISBN: 0323986056

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Virtual Screening and Drug Docking, Volume 59 in the Annual Reports on Medicinal Chemistry series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including Can docking scoring functions guarantee success in virtual screening?, No dance, no partner! A tale of flexibility in docking and virtual screening, Handling Imbalance Data in Virtual Screening, Rational computational approaches to predict novel drug candidates against leishmaniasis, Virtual screening against Mtb DNA gyrase: Applications and success stories, Using Filters in Virtual Screening: A Brief Guide to Minimize Errors and Maximize Efficiency, and more. Additional chapters in the new release include Machine Learning and Deep Learning Strategies for Virtual Screening, Applications of the Virtual Screening to find the novel HIV-1 therapeutic agents, and Large-scale screening of small molecules with docking strategies and its impact on drug discovery. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Annual Reports on Medicinal Chemistry series Updated release includes the latest information on Virtual Screening and Drug Docking


Virtual Screening for Chemists

Virtual Screening for Chemists
Author: Ishika Saha
Publisher: American Chemical Society
Total Pages: 126
Release: 2021-07-30
Genre: Science
ISBN: 0841299137

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Virtual Screening for Chemists focuses the discussion on principles underlying the most widely used methods for virtual screening today. References for more technical details have been provided where relevant. The authors have paid special attention to highlighting resources that are readily accessible to the academic community and hope these will facilitate your research aims. Demonstrative workflows have been included at the end of the e-book to allow you to familiarize yourself with the general steps involved in a virtual library screening pipeline. Familiarity with basic python and command line interface may be helpful in these examples, but scripts and execution instructions have been provided to guide you through the entire workflow. The input datasets used in the demonstrative examples are derived from the authors’ in-house virtual library, but the exercises may be adapted to other datasets of the reader’s choice.


Virtual Screening

Virtual Screening
Author: Christoph Sotriffer
Publisher: John Wiley & Sons
Total Pages: 774
Release: 2011-03-31
Genre: Medical
ISBN: 3527633340

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Drug discovery is all about finding small molecules that interact in a desired way with larger molecules, namely proteins and other macromolecules in the human body. If the three-dimensional structures of both the small and large molecule are known, their interaction can be tested by computer simulation with a reasonable degree of accuracy. Alternatively, if active ligands are already available, molecular similarity searches can be used to find new molecules. This virtual screening can even be applied to compounds that have yet to be synthesized, as opposed to "real" screening that requires cost- and labor-intensive laboratory testing with previously synthesized drug compounds. Unique in its focus on the end user, this is a real "how to" book that does not presuppose prior experience in virtual screening or a background in computational chemistry. It is both a desktop reference and practical guide to virtual screening applications in drug discovery, offering a comprehensive and up-to-date overview. Clearly divided into four major sections, the first provides a detailed description of the methods required for and applied in virtual screening, while the second discusses the most important challenges in order to improve the impact and success of this technique. The third and fourth, practical parts contain practical guidelines and several case studies covering the most important scenarios for new drug discovery, accompanied by general guidelines for the entire workflow of virtual screening studies. Throughout the text, medicinal chemists from academia, as well as from large and small pharmaceutical companies report on their experience and pass on priceless practical advice on how to make best use of these powerful methods.


Docking Screens for Drug Discovery

Docking Screens for Drug Discovery
Author: Walter Filgueira de Azevedo Jr.
Publisher: Humana
Total Pages: 286
Release: 2019-08-27
Genre: Medical
ISBN: 9781493997510

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This book focuses on recent developments in docking simulations for target proteins with chapters on specific techniques or applications for docking simulations, including the major docking programs. Additionally, the volume explores the scoring functions developed for the analysis of docking results and to predict ligand-binding affinity as well as the importance of docking simulations for the initial stages of drug discovery. Written for the highly successful Methods in Molecular Biology series, this collection presents the kind of detail and key implementation advice to ensure successful results. Authoritative and practical, Docking Screens for Drug Discovery aims to serve those interested in molecular docking simulation and also in the application of these methodologies for drug discovery.


Protein Homeostasis Diseases

Protein Homeostasis Diseases
Author: Angel L. Pey
Publisher: Academic Press
Total Pages: 450
Release: 2020-02-13
Genre: Science
ISBN: 0128191333

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Protein Homeostasis Diseases: Mechanisms and Novel Therapies offers an interdisciplinary examination of the fundamental aspects, biochemistry and molecular biology of protein homeostasis disease, including the use of natural and pharmacological small molecules to treat common and rare protein homeostasis disorders. Contributions from international experts discuss the biochemical and genetic components of protein homeostasis disorders, the mechanisms by which genetic variants may cause loss-of-function and gain-of-toxic-function, and how natural ligands can restore protein function and homeostasis in genetic diseases. Applied chapters provide guidance on employing high throughput sequencing and screening methodologies to develop pharmacological chaperones and repurpose approved drugs to treat protein homeostasis disorders. Provides an interdisciplinary examination of protein homeostasis disorders, with an emphasis on treatment strategies employing small natural and pharmacological ligands Offers applied approaches in employing high throughput sequencing and screening to develop pharmacological chaperones to treat protein homeostasis disease Gathers expertise from a range of international chapter authors who work across various biological methods and disease specific disciplines of relevance


Computational and Structural Approaches to Drug Discovery

Computational and Structural Approaches to Drug Discovery
Author: Robert M. Stroud
Publisher: Royal Society of Chemistry
Total Pages: 171
Release: 2008
Genre: Medical
ISBN: 0854043659

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This insightful book represents the experience and understanding of the global experts in the field and spotlights both the structural and medicinal chemistry aspects of drug design. The need to 'encode' the physiological factors of pharmacology, a key area, is explored.


Protein-Ligand Interactions

Protein-Ligand Interactions
Author: Holger Gohlke
Publisher: John Wiley & Sons
Total Pages: 361
Release: 2012-05-21
Genre: Medical
ISBN: 3527329668

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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.


Computation in BioInformatics

Computation in BioInformatics
Author: S. Balamurugan
Publisher: John Wiley & Sons
Total Pages: 354
Release: 2021-10-19
Genre: Computers
ISBN: 1119654718

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COMPUTATION IN BIOINFORMATICS Bioinformatics is a platform between the biology and information technology and this book provides readers with an understanding of the use of bioinformatics tools in new drug design. The discovery of new solutions to pandemics is facilitated through the use of promising bioinformatics techniques and integrated approaches. This book covers a broad spectrum of the bioinformatics field, starting with the basic principles, concepts, and application areas. Also covered is the role of bioinformatics in drug design and discovery, including aspects of molecular modeling. Some of the chapters provide detailed information on bioinformatics related topics, such as silicon design, protein modeling, DNA microarray analysis, DNA-RNA barcoding, and gene sequencing, all of which are currently needed in the industry. Also included are specialized topics, such as bioinformatics in cancer detection, genomics, and proteomics. Moreover, a few chapters explain highly advanced topics, like machine learning and covalent approaches to drug design and discovery, all of which are significant in pharma and biotech research and development. Audience Researchers and engineers in computation biology, information technology, bioinformatics, drug design, biotechnology, pharmaceutical sciences.


DOVIS: An Implementation for High-Throughput Virtual Screening Using Auto-Dock

DOVIS: An Implementation for High-Throughput Virtual Screening Using Auto-Dock
Author:
Publisher:
Total Pages: 5
Release: 2008
Genre:
ISBN:

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Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial. We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried. DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.