Download or read book Virtual Screening in Drug Discovery written by Juan Alvarez and published by CRC Press. This book was released on 2005-03-24 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Virtual Screening for Chemists written by Ishika Saha and published by American Chemical Society. This book was released on 2021-07-30 with total page 126 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Docking Screens for Drug Discovery written by Walter Filgueira de Azevedo Jr. and published by Humana. This book was released on 2019-08-27 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Protein Homeostasis Diseases written by Angel L. Pey and published by Academic Press. This book was released on 2020-02-13 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Virtual Screening written by Christoph Sotriffer and published by John Wiley & Sons. This book was released on 2011-03-31 with total page 774 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Protein Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-05-21 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Computational and Structural Approaches to Drug Discovery written by Robert M. Stroud and published by Royal Society of Chemistry. This book was released on 2008 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Data Analysis Machine Learning and Applications written by Christine Preisach and published by Springer Science & Business Media. This book was released on 2008-04-13 with total page 714 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data analysis and machine learning are research areas at the intersection of computer science, artificial intelligence, mathematics and statistics. They cover general methods and techniques that can be applied to a vast set of applications such as web and text mining, marketing, medical science, bioinformatics and business intelligence. This volume contains the revised versions of selected papers in the field of data analysis, machine learning and applications presented during the 31st Annual Conference of the German Classification Society (Gesellschaft für Klassifikation - GfKl). The conference was held at the Albert-Ludwigs-University in Freiburg, Germany, in March 2007.

Download or read book Chemoinformatics Approaches to Virtual Screening written by Alexandre Varnek and published by Royal Society of Chemistry. This book was released on 2008 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemoinformatics is broadly a scientific discipline encompassing the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information. It is distinct from other computational molecular modeling approaches in that it uses unique representations of chemical structures in the form of multiple chemical descriptors; has its own metrics for defining similarity and diversity of chemical compound libraries; and applies a wide array of statistical, data mining and machine learning techniques to very large collections of chemical compounds in order to establish robust relationships between chemical structure and its physical or biological properties. Chemoinformatics addresses a broad range of problems in chemistry and biology; however, the most commonly known applications of chemoinformatics approaches have been arguably in the area of drug discovery where chemoinformatics tools have played a central role in the analysis and interpretation of structure-property data collected by the means of modern high throughput screening. Early stages in modern drug discovery often involved screening small molecules for their effects on a selected protein target or a model of a biological pathway. In the past fifteen years, innovative technologies that enable rapid synthesis and high throughput screening of large libraries of compounds have been adopted in almost all major pharmaceutical and biotech companies. As a result, there has been a huge increase in the number of compounds available on a routine basis to quickly screen for novel drug candidates against new targets/pathways. In contrast, such technologies have rarely become available to the academic research community, thus limiting its ability to conduct large scale chemical genetics or chemical genomics research. However, the landscape of publicly available experimental data collection methods for chemoinformatics has changed dramatically in very recent years. The term "virtual screening" is commonly associated with methodologies that rely on the explicit knowledge of three-dimensional structure of the target protein to identify potential bioactive compounds. Traditional docking protocols and scoring functions rely on explicitly defined three dimensional coordinates and standard definitions of atom types of both receptors and ligands. Albeit reasonably accurate in many cases, conventional structure based virtual screening approaches are relatively computationally inefficient, which has precluded them from screening really large compound collections. Significant progress has been achieved over many years of research in developing many structure based virtual screening approaches. This book is the first monograph that summarizes innovative applications of efficient chemoinformatics approaches towards the goal of screening large chemical libraries. The focus on virtual screening expands chemoinformatics beyond its traditional boundaries as a synthetic and data-analytical area of research towards its recognition as a predictive and decision support scientific discipline. The approaches discussed by the contributors to the monograph rely on chemoinformatics concepts such as: -representation of molecules using multiple descriptors of chemical structures -advanced chemical similarity calculations in multidimensional descriptor spaces -the use of advanced machine learning and data mining approaches for building quantitative and predictive structure activity models -the use of chemoinformatics methodologies for the analysis of drug-likeness and property prediction -the emerging trend on combining chemoinformatics and bioinformatics concepts in structure based drug discovery The chapters of the book are organized in a logical flow that a typical chemoinformatics project would follow - from structure representation and comparison to data analysis and model building to applications of structure-property relationship models for hit identification and chemical library design. It opens with the overview of modern methods of compounds library design, followed by a chapter devoted to molecular similarity analysis. Four sections describe virtual screening based on the using of molecular fragments, 2D pharmacophores and 3D pharmacophores. Application of fuzzy pharmacophores for libraries design is the subject of the next chapter followed by a chapter dealing with QSAR studies based on local molecular parameters. Probabilistic approaches based on 2D descriptors in assessment of biological activities are also described with an overview of the modern methods and software for ADME prediction. The book ends with a chapter describing the new approach of coding the receptor binding sites and their respective ligands in multidimensional chemical descriptor space that affords an interesting and efficient alternative to traditional docking and screening techniques. Ligand-based approaches, which are in the focus of this work, are more computationally efficient compared to structure-based virtual screening and there are very few books related to modern developments in this field. The focus on extending the experiences accumulated in traditional areas of chemoinformatics research such as Quantitative Structure Activity Relationships (QSAR) or chemical similarity searching towards virtual screening make the theme of this monograph essential reading for researchers in the area of computer-aided drug discovery. However, due to its generic data-analytical focus there will be a growing application of chemoinformatics approaches in multiple areas of chemical and biological research such as synthesis planning, nanotechnology, proteomics, physical and analytical chemistry and chemical genomics.

Download or read book Computational Drug Discovery and Design written by and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition provides new and updated methods and techniques for identification of drug target, binding sites prediction, high- throughput virtual screening, lead discovery and optimization, conformational sampling, prediction of pharmacokinetic properties using computer-based methodologies. Chapters also focus on the application of the latest artificial intelligence technologies for computer aided drug discovery. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.

Download or read book Drug Discovery and Development written by Vishwanath Gaitonde and published by BoD – Books on Demand. This book was released on 2020-03-11 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of drug discovery and development is a complex multistage logistics project spanned over 10-15 years with an average budget exceeding 1 billion USD. Starting with target identification and synthesizing anywhere between 10k to 15k synthetic compounds to potentially obtain the final drug that reaches the market involves a complicated maze with multiple inter- and intra-operative fields. Topics described in this book emphasize the progresses in computational applications, pharmacokinetics advances, and molecular modeling developments. In addition the book also contains special topics describing target deorphaning in Mycobacterium tuberculosis, therapy treatment of some rare diseases, and developments in the pediatric drug discovery process.

Download or read book Methods and Algorithms for Molecular Docking Based Drug Design and Discovery written by Dastmalchi, Siavoush and published by IGI Global. This book was released on 2016-05-03 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: The role of technology in the medical field has resulted in significant developments within the pharmaceutical industry. Computational approaches have emerged as a crucial method in further advancing drug design and development. Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery presents emerging research on the application of computer-assisted design methods for drugs, emphasizing the benefits and improvements that molecular docking has caused within the pharmaceutical industry. Focusing on validation methods, search algorithms, and scoring functions, this book is a pivotal resource for professionals, researchers, students, and practitioners in the field of theoretical and computational chemistry.

Download or read book Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment written by Kunal Roy and published by Academic Press. This book was released on 2015-03-03 with total page 494 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment describes the historical evolution of quantitative structure-activity relationship (QSAR) approaches and their fundamental principles. This book includes clear, introductory coverage of the statistical methods applied in QSAR and new QSAR techniques, such as HQSAR and G-QSAR. Containing real-world examples that illustrate important methodologies, this book identifies QSAR as a valuable tool for many different applications, including drug discovery, predictive toxicology and risk assessment. Written in a straightforward and engaging manner, this is the ideal resource for all those looking for general and practical knowledge of QSAR methods. - Includes numerous practical examples related to QSAR methods and applications - Follows the Organization for Economic Co-operation and Development principles for QSAR model development - Discusses related techniques such as structure-based design and the combination of structure- and ligand-based design tools

Download or read book Applied Chemoinformatics written by Thomas Engel and published by John Wiley & Sons. This book was released on 2018-06-05 with total page 660 pages. Available in PDF, EPUB and Kindle. Book excerpt: Edited by world-famous pioneers in chemoinformatics, this is a clearly structured and applications-oriented approach to the topic, providing up-to-date and focused information on the wide range of applications in this exciting field. The authors explain methods and software tools, such that the reader will not only learn the basics but also how to use the different software packages available. Experts describe applications in such different fields as structure-spectra correlations, virtual screening, prediction of active sites, library design, the prediction of the properties of chemicals, the development of new cosmetics products, quality control in food, the design of new materials with improved properties, toxicity modeling, assessment of the risk of chemicals, and the control of chemical processes. The book is aimed at advanced students as well as lectures but also at scientists that want to learn how chemoinformatics could assist them in solving their daily scientific tasks. Together with the corresponding textbook Chemoinformatics - Basic Concepts and Methods (ISBN 9783527331093) on the fundamentals of chemoinformatics readers will have a comprehensive overview of the field.

Download or read book Virtual Screening and Drug Docking written by and published by Academic Press. This book was released on 2022-11-23 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Structure Based Drug Design written by Pandi Veerapandian and published by Routledge. This book was released on 2018-03-29 with total page 665 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing the most recent advances in crystallography, nuclear magnetic resonance, molecular modeling techniques, and computational combinatorial chemistry, this unique, interdisciplinary reference explains the application of three-dimensional structural information in the design of pharmaceutical drugs. Furnishing authoritative analyses by world-renowned experts, Structure-Based Drug Design discusses protein structure-based design in optimizing HIV protease inhibitors and details the biochemical, genetic, and clinical data on HIV-1 reverse transcriptase presents recent results on the high-resolution three-dimensional structure of the catalytic core domain of HIV-1 integrase as a foundation for divergent combination therapy focuses on structure-based design strategies for uncovering receptor antagonists to treat inflammatory diseases demonstrates a systematic approach to the design of inhibitory compounds in cancer treatment reviews current knowledge on the Interleukin-1 (IL-1) system and progress in the development of IL-1 modulators describes the influence of structure-based methods in designing capsid-binding inhibitors for relief of the common cold and much more!