Concepts and Experimental Protocols of Modelling and Informatics in Drug Design Book

Concepts and Experimental Protocols of Modelling and Informatics in Drug Design

  • Author : Om Silakari
  • Publisher : Academic Press
  • Release Date : 2020-11-05
  • Genre: Business & Economics
  • Pages : 396
  • ISBN 10 : 9780128205471

Concepts and Experimental Protocols of Modelling and Informatics in Drug Design Excerpt :

Concepts and Experimental Protocols of Modelling and Informatics in Drug Design discusses each experimental protocol utilized in the field of bioinformatics, focusing especially on computer modeling for drug development. It helps the user in understanding the field of computer-aided molecular modeling (CAMM) by presenting solved exercises and examples. The book discusses topics such as fundamentals of molecular modeling, QSAR model generation, protein databases and how to use them to select and analyze protein structure, and pharmacophore modeling for drug targets. Additionally, it discusses data retrieval system, molecular surfaces, and freeware and online servers. The book is a valuable source for graduate students and researchers on bioinformatics, molecular modeling, biotechnology and several members of biomedical field who need to understand more about computer-aided molecular modeling. Presents exercises with solutions to aid readers in validating their own protocol Brings a thorough interpretation of results of each exercise to help readers compare them to their own study Explains each parameter utilized in the algorithms to help readers understand and manipulate various features of molecules and target protein to design their study

Pharmacology of Drug Stereoisomers Book

Pharmacology of Drug Stereoisomers

  • Author : Alexander A. Spasov
  • Publisher : Springer Nature
  • Release Date : 2022-09-10
  • Genre: Medical
  • Pages : 218
  • ISBN 10 : 9789811923203

Pharmacology of Drug Stereoisomers Excerpt :

The book is devoted to an important aspect of pharmacology and pharmaceutical chemistry, i.e. the significance of stereoisomerism of drugs for their biological effect from the point of view of their pharmacokinetics, pharmacodynamics and toxicology. The authors review the landmarks in the development of stereochemistry and stereopharmacology. Present-day IUPAC terminology is discussed; general issues of stereoisomerism are considered including separation of racemic mixtures and asymmetric synthesis of isomers, methods of quantifying the isomers of a drug in biological material. The authors put special emphasis on general problems of the influence of stereoisomerism on pharmacological and adverse effects of drugs. A classification of drugs based on stereochemical properties of their isomers is proposed. Possibilities of interaction of stereoisomers in racemic mixtures are discussed. A considerable portion of the book is devoted to pharmacological action of the main groups of drugs whose structure includes asymmetric atoms (that is, drugs with several isomers). Detailed attention is paid to advisability of developing single isomer drugs and to the specifics of their study at the stage of preclinical and clinical trials.

Molecular Docking for Computer Aided Drug Design Book

Molecular Docking for Computer Aided Drug Design

  • Author : S. Mohane Coumar
  • Publisher : Academic Press
  • Release Date : 2021-02-17
  • Genre: Medical
  • Pages : 520
  • ISBN 10 : 9780128223130

Molecular Docking for Computer Aided Drug Design 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

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences Book

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences

  • Author : Navneet Sharma
  • Publisher : Academic Press
  • Release Date : 2021-05-21
  • Genre: Business & Economics
  • Pages : 510
  • ISBN 10 : 9780128217474

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences Excerpt :

Chemoinformatics and Bioinformatics in the Pharmaceutical Sciences brings together two very important fields in pharmaceutical sciences that have been mostly seen as diverging from each other: chemoinformatics and bioinformatics. As developing drugs is an expensive and lengthy process, technology can improve the cost, efficiency and speed at which new drugs can be discovered and tested. This book presents some of the growing advancements of technology in the field of drug development and how the computational approaches explained here can reduce the financial and experimental burden of the drug discovery process. This book will be useful to pharmaceutical science researchers and students who need basic knowledge of computational techniques relevant to their projects. Bioscientists, bioinformaticians, computational scientists, and other stakeholders from industry and academia will also find this book helpful. Provides practical information on how to choose and use appropriate computational tools Presents the wide, intersecting fields of chemo-bio-informatics in an easily-accessible format Explores the fundamentals of the emerging field of chemoinformatics and bioinformatics

Chemoinformatics Approaches to Virtual Screening Book

Chemoinformatics Approaches to Virtual Screening

  • Author : Alexandre Varnek
  • Publisher : Royal Society of Chemistry
  • Release Date : 2008
  • Genre: Science
  • Pages : 338
  • ISBN 10 : 9780854041442

Chemoinformatics Approaches to Virtual Screening 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 "

Molecular Modeling in Drug Design Book

Molecular Modeling in Drug Design

  • Author : Rebecca Wade
  • Publisher : MDPI
  • Release Date : 2019-03-26
  • Genre: Science
  • Pages : 220
  • ISBN 10 : 9783038976141

Molecular Modeling in Drug Design Excerpt :

Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power and structural and biological information of active compounds and potential target molecules. Nowadays, molecular modeling can be considered to be an integral component of the modern drug discovery and development toolbox. Nevertheless, there are still many methodological challenges to be overcome in the application of molecular modeling approaches to drug discovery. The eight original research and five review articles collected in this book provide a snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges. The topics covered include virtual screening and pharmacophore modelling, chemoinformatic applications of artificial intelligence and machine learning, molecular dynamics simulation and enhanced sampling to investigate contributions of molecular flexibility to drug–receptor interactions, the modeling of drug–receptor solvation, hydrogen bonding and polarization, and drug design against protein–protein interfaces and membrane protein receptors.

Quantitative Molecular Pharmacology and Informatics in Drug Discovery Book

Quantitative Molecular Pharmacology and Informatics in Drug Discovery

  • Author : Michael Lutz
  • Publisher : John Wiley & Sons
  • Release Date : 2000-01-10
  • Genre: Medical
  • Pages : 438
  • ISBN 10 : 0471988618

Quantitative Molecular Pharmacology and Informatics in Drug Discovery Excerpt :

Quantitative Molecular Pharmacology and Informatics in Drug Discovery Michael Lutz, Section Head, Cheminformatics Group and Terry Kenakin, Principal Research Scientist, Glaxo Wellcome Research and Development, Research Triangle Park, NC, USA Quantitative Molecular Pharmacology and Informatics in Drug Discovery combines pharmacology, genetics and statistics to provide a complete guide to the modern drug discovery process. The book discusses the pharmacology of drug testing and provides a detailed description of the statistical methods used to analyze the resulting data. Application of genetic and genomic tools for identification of biological targets is reviewed in the context of drug discovery projects. Covering both the theoretical principles upon which the techniques are based and the practicalities of drug discovery, this informative guide. * outlines in step-by-step detail the advantages and disadvantages of each technology and approach and links these to the type of chemical target being sought after in the drug discovery process; and, * provides excellent demonstrations of how to use powerful pharmacological and statistical tools to optimize high-throughput screening assays. Written by two internationally known and well-regarded experts, this book is an essential reference for research and development scientists working in the pharmaceutical and biotechnology industries. It will also be useful for postgraduates studying pharmacology and applied statistics.

Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment Book

Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment

  • Author : Kunal Roy
  • Publisher : Academic Press
  • Release Date : 2015-03-03
  • Genre: Medical
  • Pages : 484
  • ISBN 10 : 9780128016336

Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment 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

Current Methods In Medicinal Chemistry And Biological Physics Book

Current Methods In Medicinal Chemistry And Biological Physics

  • Author : Carlton A. Taft
  • Publisher : Unknown
  • Release Date : 2008-01-01
  • Genre: Biophysics
  • Pages : 247
  • ISBN 10 : 8130802929

Current Methods In Medicinal Chemistry And Biological Physics Excerpt :

This book is aimed at, from students to advanced researchers, for anyone that is interested or works with current experimental and theoretical methods in medicinal chemistry and biological physics, with particular interest in chemoinformatics, bioinformatics, molecular modeling, QSAR, spectrometry, molecular biology and combinatorial chemistry for many therapeutic purposes. This book attempts to convey something of the fascination of working in these multidisciplinar areas, which overlap knowledge of chemistry, physics, biochemistry, biology and pharmacology. This second volume, in particular, contains 11 chapters, of which 6 are related to theoretical methods in medicinal chemistry and at least 5 deal with experimental/mixed methods. In the modern computational medicinal chemistry, quantum mechanics (QM) plays an important role since the associated methods can describe molecular energies, bond breaking or forming, charge transfer and polarization effects. Historically in drug design, QM ligand-based applications were devoted to investigations of electronic features, and they have also been routinely used in the development of quantum descriptors in quantitative structure-activity relationships (QSAR) approaches. In chapter 1, we present an overview of the state-of-the-art of quantum methods currently used in medicinal chemistry. Molecular Dynamics (MD) simulation is a sophisticated molecular modeling technique useful to describe molecular structures and macroscopic properties in very large molecular systems comprising hundreds or even thousands of atoms. In the field of drug discovery, MD simulation has been widely used to understand the biomolecule structure, drug and biomolecule interactions. The chapter 2 outlines the theory and practical details of MD approach and focuses on its application in studies of prediction of binding affinities for putative receptor-ligand complexes. In chapter 3 we discuss the important role of the homology modeling procedure in the d

Advances in Protein Molecular and Structural Biology Methods Book

Advances in Protein Molecular and Structural Biology Methods

  • Author : Timir Tripathi
  • Publisher : Academic Press
  • Release Date : 2022-01-14
  • Genre: Science
  • Pages : 714
  • ISBN 10 : 9780323902656

Advances in Protein Molecular and Structural Biology Methods Excerpt :

Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Structural Bioinformatics  Applications in Preclinical Drug Discovery Process Book

Structural Bioinformatics Applications in Preclinical Drug Discovery Process

  • Author : C. Gopi Mohan
  • Publisher : Springer
  • Release Date : 2019-01-10
  • Genre: Science
  • Pages : 406
  • ISBN 10 : 9783030052829

Structural Bioinformatics Applications in Preclinical Drug Discovery Process Excerpt :

This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery. The book offers an invaluable resource for graduate and postgraduate students, as well as for researchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

Computer Aided Drug Design Book

Computer Aided Drug Design

  • Author : Dev Bukhsh Singh
  • Publisher : Springer Nature
  • Release Date : 2020-10-09
  • Genre: Medical
  • Pages : 306
  • ISBN 10 : 9789811568152

Computer Aided Drug Design Excerpt :

This book provides up-to-date information on bioinformatics tools for the discovery and development of new drug molecules. It discusses a range of computational applications, including three-dimensional modeling of protein structures, protein-ligand docking, and molecular dynamics simulation of protein-ligand complexes for identifying desirable drug candidates. It also explores computational approaches for identifying potential drug targets and for pharmacophore modeling. Moreover, it presents structure- and ligand-based drug design tools to optimize known drugs and guide the design of new molecules. The book also describes methods for identifying small-molecule binding pockets in proteins, and summarizes the databases used to explore the essential properties of drugs, drug-like small molecules and their targets. In addition, the book highlights various tools to predict the absorption, distribution, metabolism, excretion (ADME) and toxicity (T) of potential drug candidates. Lastly, it reviews in silico tools that can facilitate vaccine design and discusses their limitations.

Biomarkers in Drug Development Book

Biomarkers in Drug Development

  • Author : Michael R. Bleavins
  • Publisher : John Wiley & Sons
  • Release Date : 2011-09-20
  • Genre: Medical
  • Pages : 784
  • ISBN 10 : 9781118210420

Biomarkers in Drug Development Excerpt :

Discover how biomarkers can boost the success rate of drugdevelopment efforts As pharmaceutical companies struggle to improve the success rateand cost-effectiveness of the drug development process, biomarkershave emerged as a valuable tool. This book synthesizes and reviewsthe latest efforts to identify, develop, and integrate biomarkersas a key strategy in translational medicine and the drugdevelopment process. Filled with case studies, the bookdemonstrates how biomarkers can improve drug development timelines,lower costs, facilitate better compound selection, reducelate-stage attrition, and open the door to personalizedmedicine. Biomarkers in Drug Development is divided into eightparts: Part One offers an overview of biomarkers and their role in drugdevelopment. Part Two highlights important technologies to help researchersidentify new biomarkers. Part Three examines the characterization and validation processfor both drugs and diagnostics, and provides practical advice onappropriate statistical methods to ensure that biomarkers fulfilltheir intended purpose. Parts Four through Six examine the application of biomarkers indiscovery, preclinical safety assessment, clinical trials, andtranslational medicine. Part Seven focuses on lessons learned and the practical aspectsof implementing biomarkers in drug development programs. Part Eight explores future trends and issues, including dataintegration, personalized medicine, and ethical concerns. Each of the thirty-eight chapters was contributed by one or moreleading experts, including scientists from biotechnology andpharmaceutical firms, academia, and the U.S. Food and DrugAdministration. Their contributions offer pharmaceutical andclinical researchers the most up-to-date understanding of thestrategies used for and applications of biomarkers in drugdevelopment.

Chemoinformatics in Drug Discovery Book
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Chemoinformatics in Drug Discovery

  • Author : Tudor I. Oprea
  • Publisher : John Wiley & Sons
  • Release Date : 2006-03-06
  • Genre: Science
  • Pages : 515
  • ISBN 10 : 9783527604203

Chemoinformatics in Drug Discovery Excerpt :

This handbook provides the first-ever inside view of today's integrated approach to rational drug design. Chemoinformatics experts from large pharmaceutical companies, as well as from chemoinformatics service providers and from academia demonstrate what can be achieved today by harnessing the power of computational methods for the drug discovery process. With the user rather than the developer of chemoinformatics software in mind, this book describes the successful application of computational tools to real-life problems and presents solution strategies to commonly encountered problems. It shows how almost every step of the drug discovery pipeline can be optimized and accelerated by using chemoinformatics tools -- from the management of compound databases to targeted combinatorial synthesis, virtual screening and efficient hit-to-lead transition. An invaluable resource for drug developers and medicinal chemists in academia and industry.

Bioinformatics Book


  • Author : Dev Bukhsh Singh
  • Publisher : Academic Press
  • Release Date : 2021-10-21
  • Genre: Business & Economics
  • Pages : 510
  • ISBN 10 : 9780323900058

Bioinformatics Excerpt :

Bioinformatics: Methods and Applications provides a thorough and detailed description of principles, methods, and applications of bioinformatics in different areas of life sciences. It presents a compendium of many important topics of current advanced research and basic principles/approaches easily applicable to diverse research settings. The content encompasses topics such as biological databases, sequence analysis, genome assembly, RNA sequence data analysis, drug design, and structural and functional analysis of proteins. In addition, it discusses computational approaches for vaccine design, systems biology and big data analysis, and machine learning in bioinformatics. It is a valuable source for bioinformaticians, computer biologists, and members of biomedical field who needs to learn bioinformatics approaches to apply to their research and lab activities. Covers basic and more advanced developments of bioinformatics with a diverse and interdisciplinary approach to fulfill the needs of readers from different backgrounds Explains in a practical way how to decode complex biological problems using computational approaches and resources Brings case studies, real-world examples and several protocols to guide the readers with a problem-solving approach