Download or read book Beginner s Guide to Protein Ligand Docking Using Autodock Vina written by Vishal Mevada and published by . This book was released on 2017-07-21 with total page 54 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 analyse Protein Ligand Bindind 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. The book is totally associated with the three step simple tutorial for beginners to start his researchwork using Autodock vina.
Download or read book Basic Biotechniques for Bioprocess and Bioentrepreneurship written by Arvind Kumar Bhatt and published by Academic Press. This book was released on 2023-02-03 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: Basic Biotechniques for Bioprocess and Bioentrepreneurship deals with the entire field of industrial biotechnology, starting from the basic laboratory techniques to scale-up, process development, demonstration, and finally its commercialization. The book compiles currently scattered materials on this topic and updates this information based on practical experience and requirements. The book will be an ideal source for new entrepreneurs who wish to start their own commercial units. Offers guidance for readers/researchers/start-ups/entrepreneurs on how to develop new microbiological and biotechnical processes Focuses on basic knowledge and possible solutions to the practical difficulties at all levels in one place through understanding of basic techniques in lab, during bioprocess development, commercialization, technology transfer, marketing, and others which is presently not available in the field Provides multifaceted coverage, with industry insights from experienced practitioners and leaders in the field Gives possible best solutions to the practical difficulties at all levels, i.e. lab, scaleup, and commercial stage Addresses ethical and other regulatory issues
Download or read book Molecular Docking for Computer Aided Drug Design written by Mohane S. Coumar and published by Academic Press. This book was released on 2021-02-17 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design. The book is divided into three main sections that cover basic techniques, tools, web servers and applications. It is an essential reference for students and researchers involved in drug design and discovery. Covers the latest information and state-of-the-art trends in structure-based drug design methodologies Includes case studies that complement learning Consolidates fundamental concepts and current practice of molecular docking into one convenient resource
Download or read book ProteinProtein Interaction Regulators written by Siddhartha Roy and published by Royal Society of Chemistry. This book was released on 2020-12-14 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: New genomic information has revealed the crucial role that protein–protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein–Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.
Download or read book Protein Engineering written by Tomohisa Ogawa and published by BoD – Books on Demand. This book was released on 2013-05-29 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: Given the centrality of protein to many biological process, this book makes a significant contribution to the fields of healthcare and nutrition. Its chapters consider topics such as protein-protein and protein-ligand docking, and the protein engineering of enzymes involved in bioplastic metabolism. One contribution gives an overview of the In Vitro Virus (IVV) analytic method, while another shows how cutting-edge techniques in protein engineering advance our knowledge in the field of palaeontology. The book also includes a review of classic and alternative strategies when using yeasts in research, with a focus on Pichia pastoris as a host. Finally, there are two contributions on chromatography: one on the method itself, and another on its use to identify HMGB1-binding components.
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 2020-08-27 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 Computational Drug Discovery and Design written by Mohini Gore and published by Springer Nature. This book was released on 2023-10-09 with total page 357 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. Authoritative and cutting-edge, Computational Drug Discovery and Design, Second Edition aims to effectively utilize computational methodologies in discovery and design of novel drugs.
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 Molecular Docking written by Dimitrios Vlachakis and published by BoD – Books on Demand. This book was released on 2018-07-11 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular docking has always been and will be on the forefront of developments in the eminent field of drug design and medicinal chemistry. At the early days, drug discovery was based on blackboard drawings and expert intuition. However, as times move on, the amount of available information and overall knowledge base that needs to be analyzed cannot be processed manually. This, coupled by the rapid growth in computational infrastructure and processing power, has allowed for the efficient use of molecular docking tools and algorithms to be considered in the greater field of drug discovery. In the postgenomic era, molecular docking has become the key player for the screening of hundreds of thousands of compounds against a repertoire of pharmacological targets.
Download or read book Protein Modelling written by Andrew Gamble and published by Springer. This book was released on 2014-11-13 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.
Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
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 Modeling Peptide Protein Interactions written by Ora Schueler-Furman and published by Humana. This book was released on 2017-02-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume covers an array of techniques available for studying peptide-protein docking and design. The book is divided into four sections: peptide binding site prediction; peptide-protein docking; prediction and design of peptide binding specificity; and the design of inhibitory peptides. The chapters in Modeling Peptide-Protein Interactions: Methods and Protocols cover topics such as the usage of ACCLUSTER and PeptiMap for peptide binding site prediction; AnchorDock and ATTRACT for blind, flexible docking of peptides to proteins; flexible peptide docking using HADDOCK and FlexPepDock; identifying loop-mediated protein-protein interactions using LoopFinder; and protein-peptide interaction design using PinaColada. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary details for successful application of the different approaches and step-by-step, readily reproducible protocols, as well as tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Modeling Peptide-Protein Interactions: Methods and Protocols provides a diverse and unified overview of this rapidly advancing field of major interest and applicability.
Download or read book Proteases in Human Diseases written by Sajal Chakraborti and published by Springer. This book was released on 2017-07-13 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book bridges the gap between fundamental research and biomedical and pharmacological applications on proteases. It represents a comprehensive overview of the multifaceted field of proteases in cellular environment and highlights the recently elucidated functions of complex proteolytic systems in different diseases. Several established investigators have elucidated the crucial role of proteases in biological processes, including how proteolytic function and regulation can be combined to develop new strategies of therapeutic interventions. Proteases form one of the largest and most diverse families of enzymes known. It is now clear that proteases are involved in every aspect of life functions of an organism. Under physiological conditions, proteases are regulated by their endogenous inhibitors; however, when the activity of proteases is not regulated appropriately, disease processes can result in. So, there is absolute need for a stringent control of proteolytic activities in cells and tissues. Dysregulation of proteases may cause derangement of cellular signalling network resulting in different pathophysiological conditions such as vascular remodelling, atherosclerotic plaque progression, ulcer and rheumatoid arthritis, Alzheimer disease, cancer metastasis, tumor progression and inflammation. Additionally, many infective microorganisms require proteases for replication or use proteases as virulence factors, which have facilitated the development of protease-targeted therapies for a variety of parasitic diseases.
Download or read book In Silico Drug Design written by Kunal Roy and published by Academic Press. This book was released on 2019-02-12 with total page 886 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Drug Design: Repurposing Techniques and Methodologies explores the application of computational tools that can be utilized for this approach. The book covers theoretical background and methodologies of chem-bioinformatic techniques and network modeling and discusses the various applied strategies to systematically retrieve, integrate and analyze datasets from diverse sources. Other topics include in silico drug design methods, computational workflows for drug repurposing, and network-based in silico screening for drug efficacy. With contributions from experts in the field and the inclusion of practical case studies, this book gives scientists, researchers and R&D professionals in the pharmaceutical industry valuable insights into drug design. Discusses the theoretical background and methodologies of useful techniques of cheminformatics and bioinformatics that can be applied for drug repurposing Offers case studies relating to the in silico modeling of FDA-approved drugs for the discovery of antifungal, anticancer, antiplatelet agents, and for drug therapies against diseases Covers tools and databases that can be utilized to facilitate in silico methods for drug repurposing
Download or read book Science Gateways for Distributed Computing Infrastructures written by Péter Kacsuk and published by Springer. This book was released on 2014-10-28 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book describes the science gateway building technology developed in the SCI-BUS European project and its adoption and customization method, by which user communities, such as biologists, chemists, and astrophysicists, can build customized, domain-specific science gateways. Many aspects of the core technology are explained in detail, including its workflow capability, job submission mechanism to various grids and clouds, and its data transfer mechanisms among several distributed infrastructures. The book will be useful for scientific researchers and IT professionals engaged in the development of science gateways.
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!
