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This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead to the discovery of new medicines.
This book focuses on applications of compound library design and virtual screening to expand the bioactive chemical space, to target hopping of chemotypes to identify synergies within related drug discovery projects or to repurpose known drugs, to propose mechanism of action of compounds, or to identify off-target effects by cross-reactivity analysis. Both ligand-based and structure-based in silico approaches, as reviewed in this book, play important roles for all these applications. Computational chemogenomics is expected to increase the quality and productivity of drug discovery and lead to the discovery of new medicines.
Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information
In the post-genomic era, one of the key challenges for drug discovery is making optimal use of the comprehensive genomic data available after the elucidation of the human genome and others in order to identify effective new medicines. Addressing this challenge, chemogenomics aims to identify systematically all ligands and modulators for all the gene products expressed and allows the accelerated exploration of their biological function. The subject brings together diverse disciplines including chemistry, genetics, chemo- and bioinformatics, structural biology, and biological screening in phenotypic and target-based assays. This book uniquely integrates reviews of the latest cutting-edge research by leaders in the various disciplines, providing a general, knowledge-centric overview of the different chemical, biological and informatics components. Unlike existing publications, the book focuses on how these disciplines interact efficiently for the rapid discovery of new targets and their effector molecules simultaneously. Examples of chemogenomics approaches pursued in academia as well as in biotech and pharmaceutical companies are also provided. Contents: Small Molecules for Chemogenomics-based Drug Discovery (E Jacoby et al.)Mapping the Chemogenomic Space (J Mestres)Natural Product Scaffolds and Protein Structure Similarity Clustering (PSSC) as Inspiration Sources for Compound Library Design in Chemogenomics and Drug Development (F J Dekker et al.)A Reductionist Approach to Chemogenomics in the Design of Drug Molecules and Focused Libraries (R Crossley & M Slater)In silico Screening of the Protein Structure Repertoire and of Protein Families (D Rognan)New Methods for Smilarity-based Virtual Screening (J Hert et al.)Structural Informatics: Chemogenomics In silico (D A Debe et al.)Construction of a Homogenous and Informative In vitro Profiling Database for Anticipating the Clinical Effects of Drugs (N Froloff et al.)The Inpharmatica Pharmacata Approach (J Overinghton)Target- and Cell-Based Assays and Screening: Reverse Chemogenomics (R Bouhelal & D Frabbro) Readership: Undergraduate and graduate students, and researchers in molecular pharmacology, pharmacy, medicinal chemistry, molecular and structural biology, drug discovery, genomics, bioinformatics. Key Features:Provides a unique overview of state-of-the-art chemogenomics knowledge-based approaches for target and drug identificationWritten by leading scientists in the various disciplines involved in chemogenomicsKeywords:Chemogenomics;Drug Discovery;Medicinal Chemistry;Knowledge-Based Approaches;Design of Compound Screening Collections;Natural Products;Target Families;Chemoinformatics;Bioinformatics;Mode of Action Profiling
Chemogenomics and Chemical Genetics by ERIC MARECHAL,Sylvaine Roy,Laurence Lafanechère Pdf
Biological and chemical sciences have undergone an unprecedented transformation, reflected by the huge use of parallel and automated technologies in key fields such as genome sequencing, DNA chips, nanoscale functional biology or combinatorial chemistry. It is now possible to generate and store from tens of thousands to millions of new small molecules, based on enhanced chemical synthesis strategies. Automated screening of small molecules is one of the technologies that has revolutionized biology, first developed for the pharmaceutical industry and recently introduced in academic laboratories. High-throughput and high-content screening allow the identification of bioactive compounds in collections of molecules (chemical libraries), being effective on biological targets defined at various organisational scales, from proteins to cells to complete organisms. These bioactive molecules can be therapeutic drug candidates, molecules for biotech, diagnostic or agronomic applications, or tools for basic research. Handling a large number of biological (genomic and post-genomic), chemical and experimental information, screening approaches cannot be envisaged without any electronic storage and mathematical treatment of the data. “Chemogenomics and Chemical Genetics” is an introductory manual presenting methods and concepts making up the basis for this recent discipline. This book is dedicated to biologists, chemists and computer scientist beginners. It is organized in brief, illustrated chapters with practical examples. Clear definitions of biological, chemical and IT concepts are given in a glossary section to help readers who are not familiar with one of these disciplines. "Chemogenomics and Chemical Genetics" should therefore be helpful for students (from Bachelor's degree level), technological platform engineers, and researchers in biology, chemistry, bioinformatics, cheminformatics, both in biotech and academic laboratories.
Computational Immunology: Applications focuses on different mathematical models, statistical tools, techniques, and computational modelling that helps in understanding complex phenomena of the immune system and its biological functions. The book also focuses on the latest developments in computational biology in designing of drugs, targets, biomarkers for early detection and prognosis of a disease. It highlights the applications of computational methods in deciphering the complex processes of the immune system and its role in health and disease. This book discusses the most essential topics, including Next generation sequencing (NGS) and computational immunology Computational modelling and biology of diseases Drug designing Computation and identification of biomarkers Application in organ transplantation Application in disease detection and therapy Computational methods and applications in understanding of the invertebrate immune system S Ghosh is MSc, PhD, PGDHE, PGDBI, is PhD from IICB, CSIR, Kolkata, awarded the prestigious National Scholarship from the Government of India. She has worked and published extensively in glycobiology, sialic acids, immunology, stem cells and nanotechnology. She has authored several publications that include books and encyclopedia chapters in reputed journals and books.
Systems and Computational Biology by Ning-Sun Yang Pdf
Whereas some "microarray" or "bioinformatics" scientists among us may have been criticized as doing "cataloging research", the majority of us believe that we are sincerely exploring new scientific and technological systems to benefit human health, human food and animal feed production, and environmental protections. Indeed, we are humbled by the complexity, extent and beauty of cross-talks in various biological systems; on the other hand, we are becoming more educated and are able to start addressing honestly and skillfully the various important issues concerning translational medicine, global agriculture, and the environment. The two volumes of this book present a series of high-quality research or review articles in a timely fashion to this emerging research field of our scientific community.
Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV2 Infection by Arpana Parihar,Raju Khan,Ashok Kumar,Ajeet Kumar Kaushik,Hardik Gohel Pdf
Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV2 Infection: Revolutionary Strategies to Combat Pandemics compiles information about various computational bioinformatic approaches that can help combat viral infection. The book includes working knowledge of various molecular docking and molecular dynamic simulation approaches that have been exploited for drug repurposing and drug designing purpose. In addition, it sheds light on reverse vaccinomics and immunoinformatic approaches for vaccine designing against SARS-CoV2 infection. This book is an essential resource for researchers, bioinformaticians, computational biologists, computational chemists and pharmaceutical companies who are working on the development of effective and specific therapeutic interventions and point-of-care diagnostic devices using various computational approaches. Covers computational based approaches for designing and repurposing drugs Discusses immunoinformatic and reverse vaccinomic approaches for effective vaccine design Categorizes information about artificial intelligence-based drug screening and diagnostic tools
Computational Intelligence in Recent Communication Networks by Mariya Ouaissa,Zakaria Boulouard,Mariyam Ouaissa,Bassma Guermah Pdf
This book focuses on the use of Artificial Intelligence and Machine Learning (AI/ML) based techniques to solve issues related to communication networks, their layers, as well as their applications. The book first offers an introduction to recent trends regarding communication networks. The authors then provide an overview of theoretical concepts of AI/ML, techniques and protocols used in different layers of communication. Furthermore, this book presents solutions that help analyze complex patterns in user data and ultimately improve productivity. Throughout, AI/ML-based solutions are provided, for topics such as signal detection, channel modeling, resource optimization, routing protocol design, transport layer optimization, user/application behavior prediction, software-defined networking, congestion control, communication network optimization, security, and anomaly detection. The book features chapters from a large spectrum of authors including researchers, students, as well as industrials involved in research and development.
Phytochemistry, Computational Tools, and Databases in Drug Discovery by Chukwuebuka Egbuna,Mithun Rudrapal,Habibu Tijjani Pdf
Phytochemistry, Computational Tools and Databases in Drug Discovery presents the state-of-the-art in computational methods and techniques for drug discovery studies from medicinal plants. Various tools and databases for virtual screening and characterization of plant bioactive compounds and their subsequent predictions on biological targets for the discovery of new drugs against specific diseases are presented, along with computational tools for the prediction of the toxic effects of phytochemicals on living systems. The book also provides in-depth insight on the applications of these computational tools as well as the databases that describe the interactions of phytochemicals with diseases along with predictions for druggable bioactive compounds. Useful for drug developers, medicinal chemists, toxicologists, phytochemists, plant biochemists and analytical chemists, this book clearly presents the various computational techniques, tools and databases for phytochemical research. Provides the various databases, methods and procedures for computational drug discovery in plants Includes insights into the predictors for properties of phytochemicals against different diseases Discusses the applications of computational tools and their databases
Advances in Computational Modeling and Simulation by Rallapalli Srinivas,Rajesh Kumar,Mainak Dutta Pdf
The book presents select proceedings of Global meet on ‘Computational Modelling and Simulation, Recent Innovations, Challenges and Perspectives, 2020. This book covers leading-edge technologies from different domains such as computation in optimization and control, multiscale and multiphysics modeling and computation analysis, environmental modeling, modeling approaches to enterprise systems and services, finite element analysis, dependability and security, high-performance computation/cloud computing applications, computational biology and chemistry and computational mechanics. The primary goal of this book is to strengthen pre-eminence in computational modeling and simulation by catalyzing the transformative use of innovative developments in a wide range of disciplines to achieve lasting societal impact. The book discusses on how to perform simulation of large complex dynamic systems in an efficient manner using advanced computational analysis. The inter-disciplinary nature of the book would be a valuable reference for academicians and research scientists, industrialists interested in modelling and simulation driven by computational technology.
Application of Computational Techniques in Pharmacy and Medicine by Leonid Gorb,Victor Kuz'min,Eugene Muratov Pdf
The proposed volume provides both fundamental and detailed information about the computational and computational-experimental studies which improve our knowledge of how leaving matter functions, the different properties of drugs (including the calculation and the design of new ones), and the creation of completely new ways of treating numerical diseases. Whenever it is possible, the interplay between theory and experiment is provided. The book features computational techniques such as quantum-chemical and molecular dynamic approaches and quantitative structure–activity relationships. The initial chapters describe the state-of-the art research on the computational investigations in molecular biology, molecular pharmacy, and molecular medicine performed with the use of pure quantum-chemical techniques. The central part of the book illustrates the status of computational techniques that utilize hybrid, so called QM/MM approximations as well as the results of the QSAR studies which now are the most popular in predicting drugs’ efficiency. The last chapters describe combined computational and experimental investigations.
The book "Drug Selectivity - An Evolving Concept in Medicinal Chemistry" provides a current overview and comprehensive compilation for medicinal chemists that discusses the effects of aiming for multiple targets on the entire drug development process. The result is a broad survey of current and future strategies for drug selectivity in medicinal chemistry with theoretical but also practical aspects. Different strategies are presented and evaluated, such as various design approaches, merged multiple ligands, discovery technologies and a broad range of successful examples of unselective drugs taken from all major disease areas. With its wide-ranging view of an emerging new paradigm in drug development, this handbook is of prime importance for every medicinal and pharmaceutical chemist.
There is a growing interest in unmet needs for the development of a new discipline in drug discovery and in university education on polypharmacology. However, there has not been a book with the comprehensive compilation of basic knowledge and advanced methodology that is needed. This book aims to meet the needs making Polypharmacology a new sub-discipline of Pharmacology, not only being a hot area of pharmacological research and education but also a new paradigm for drug discovery. It contains the contents covering the entire scope of Polypharmacology including systemic in-depth exposition of basic knowledge, novel concepts, innovative technologies, and translational and clinical applications by showcasing state-of-the-art strategies and step-by-step instructions of cutting-edge methods. The contents of this book targets broad readerships including scientists in pharmacology research and drug development, and university teachers and graduates in medical school or school of pharmacy.
Chemical Genomics and Proteomics by Ferenc Darvas,András Guttman,György Dormán Pdf
Since the publication of the pioneering first edition of Chemical Genomics and Proteomics more than seven years ago, the area of chemical genomics has rapidly expanded and diversified to numerous novel methods and subdisciplines, such as chemical glycomics and lipidomics. This second edition has been updated to uniquely reflect this interdisciplina
