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Molecular Similarity In Drug Design
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Book Synopsis Chemoinformatics for Drug Discovery by : Jürgen Bajorath
Download or read book Chemoinformatics for Drug Discovery written by Jürgen Bajorath and published by John Wiley & Sons. This book was released on 2013-09-25 with total page 483 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemoinformatics strategies to improve drug discovery results With contributions from leading researchers in academia and the pharmaceutical industry as well as experts from the software industry, this book explains how chemoinformatics enhances drug discovery and pharmaceutical research efforts, describing what works and what doesn't. Strong emphasis is put on tested and proven practical applications, with plenty of case studies detailing the development and implementation of chemoinformatics methods to support successful drug discovery efforts. Many of these case studies depict groundbreaking collaborations between academia and the pharmaceutical industry. Chemoinformatics for Drug Discovery is logically organized, offering readers a solid base in methods and models and advancing to drug discovery applications and the design of chemoinformatics infrastructures. The book features 15 chapters, including: What are our models really telling us? A practical tutorial on avoiding common mistakes when building predictive models Exploration of structure-activity relationships and transfer of key elements in lead optimization Collaborations between academia and pharma Applications of chemoinformatics in pharmaceutical research experiences at large international pharmaceutical companies Lessons learned from 30 years of developing successful integrated chemoinformatic systems Throughout the book, the authors present chemoinformatics strategies and methods that have been proven to work in pharmaceutical research, offering insights culled from their own investigations. Each chapter is extensively referenced with citations to original research reports and reviews. Integrating chemistry, computer science, and drug discovery, Chemoinformatics for Drug Discovery encapsulates the field as it stands today and opens the door to further advances.
Book Synopsis 3D QSAR in Drug Design by : Hugo Kubinyi
Download or read book 3D QSAR in Drug Design written by Hugo Kubinyi and published by Springer Science & Business Media. This book was released on 1998-04-30 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volumes 2 and 3 of the 3D QSAR in Drug Design series aim to review the progress being made in CoMFA and other 3D QSAR approaches since the publication of the highly successful first volume about four years ago. Volume 2 (Ligand-Protein Interactions and Molecular Similarity) divides into three sections dealing with Ligand-Protein Interactions, Quantum Chemical Models and Molecular Dynamics Simulations, and Pharmacophore Modelling and Molecular Similarity, respectively. Volume 3 (Recent Advances) is also divided into three sections, namely 3D QSAR Methodology: CoMFA and Related Approaches, Receptor Models and Other 3D QSAR Approaches, and 3D QSAR Applications. More than seventy distinguished scientists have contributed nearly forty reviews of their work and related research to these two volumes which are of outstanding quality and timeliness. These works present an up-to-date coverage of the latest developments in all fields of 3D QSAR.
Book Synopsis De novo Molecular Design by : Gisbert Schneider
Download or read book De novo Molecular Design written by Gisbert Schneider and published by John Wiley & Sons. This book was released on 2013-10-10 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systematically examining current methods and strategies, this ready reference covers a wide range of molecular structures, from organic-chemical drugs to peptides, Proteins and nucleic acids, in line with emerging new drug classes derived from biomacromolecules. A leader in the field and one of the pioneers of this young discipline has assembled here the most prominent experts from across the world to provide first-hand knowledge. While most of their methods and examples come from the area of pharmaceutical discovery and development, the approaches are equally applicable for chemical probes and diagnostics, pesticides, and any other molecule designed to interact with a biological system. Numerous images and screenshots illustrate the many examples and method descriptions. With its broad and balanced coverage, this will be the firststop resource not only for medicinal chemists, biochemists and biotechnologists, but equally for bioinformaticians and molecular designers for many years to come. From the content: * Reaction-driven de novo design * Adaptive methods in molecular design * Design of ligands against multitarget profiles * Free energy methods in ligand design * Fragment-based de novo design * Automated design of focused and target family-oriented compound libraries * Molecular de novo design by nature-inspired computing * 3D QSAR approaches to de novo drug design * Bioisosteres in de novo design * De novo design of peptides, proteins and nucleic acid structures, including RNA aptamers and many more.
Book Synopsis 3D QSAR in Drug Design by : Hugo Kubinyi
Download or read book 3D QSAR in Drug Design written by Hugo Kubinyi and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: Significant progress has been made in the study of three-dimensional quantitative structure-activity relationships (3D QSAR) since the first publication by Richard Cramer in 1988 and the first volume in the series, 3D QSAR in Drug Design. Theory, Methods and Applications, published in 1993. The aim of that early book was to contribute to the understanding and the further application of CoMFA and related approaches and to facilitate the appropriate use of these methods. Since then, hundreds of papers have appeared using the quickly developing techniques of both 3D QSAR and computational sciences to study a broad variety of biological problems. Again the editor(s) felt that the time had come to solicit reviews on published and new viewpoints to document the state of the art of 3D QSAR in its broadest definition and to provide visions of where new techniques will emerge or new appli- tions may be found. The intention is not only to highlight new ideas but also to show the shortcomings, inaccuracies, and abuses of the methods. We hope this book will enable others to separate trivial from visionary approaches and me-too methodology from in- vative techniques. These concerns guided our choice of contributors. To our delight, our call for papers elicited a great many manuscripts.
Book Synopsis Molecular Similarity in Drug Design by : P.M. Dean
Download or read book Molecular Similarity in Drug Design written by P.M. Dean and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular similarity searching is fast becoming a key tool in organic chemistry. In this book, the editor has brought together an international team of authors, each working at the forefront of this technology, providing a timely and concise overview of current research. The chapters focus principally on those methods which have reached sufficient maturity to be of immediate practical use in molecular design.
Book Synopsis An Introduction to Chemoinformatics by : Andrew R. Leach
Download or read book An Introduction to Chemoinformatics written by Andrew R. Leach and published by Springer. This book was released on 2007-09-04 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to provide an introduction to the major techniques of chemoinformatics. It is the first text written specifically for this field. The first part of the book deals with the representation of 2D and 3D molecular structures, the calculation of molecular descriptors and the construction of mathematical models. The second part describes other important topics including molecular similarity and diversity, the analysis of large data sets, virtual screening, and library design. Simple illustrative examples are used throughout to illustrate key concepts, supplemented with case studies from the literature.
Book Synopsis Handbook of Chemoinformatics Algorithms by : Jean-Loup Faulon
Download or read book Handbook of Chemoinformatics Algorithms written by Jean-Loup Faulon and published by CRC Press. This book was released on 2010-04-21 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Unlike in the related area of bioinformatics, few books currently exist that document the techniques, tools, and algorithms of chemoinformatics. Bringing together worldwide experts in the field, the Handbook of Chemoinformatics Algorithms provides an overview of the most common chemoinformatics algorithms in a single source.After a historical persp
Book Synopsis Drug-like Properties: Concepts, Structure Design and Methods by : Li Di
Download or read book Drug-like Properties: Concepts, Structure Design and Methods written by Li Di and published by Elsevier. This book was released on 2010-07-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: Of the thousands of novel compounds that a drug discovery project team invents and that bind to the therapeutic target, typically only a fraction of these have sufficient ADME/Tox properties to become a drug product. Understanding ADME/Tox is critical for all drug researchers, owing to its increasing importance in advancing high quality candidates to clinical studies and the processes of drug discovery. If the properties are weak, the candidate will have a high risk of failure or be less desirable as a drug product. This book is a tool and resource for scientists engaged in, or preparing for, the selection and optimization process. The authors describe how properties affect in vivo pharmacological activity and impact in vitro assays. Individual drug-like properties are discussed from a practical point of view, such as solubility, permeability and metabolic stability, with regard to fundamental understanding, applications of property data in drug discovery and examples of structural modifications that have achieved improved property performance. The authors also review various methods for the screening (high throughput), diagnosis (medium throughput) and in-depth (low throughput) analysis of drug properties. - Serves as an essential working handbook aimed at scientists and students in medicinal chemistry - Provides practical, step-by-step guidance on property fundamentals, effects, structure-property relationships, and structure modification strategies - Discusses improvements in pharmacokinetics from a practical chemist's standpoint
Book Synopsis Molecular Modelling and Drug Design by : Vintner
Download or read book Molecular Modelling and Drug Design written by Vintner and published by CRC Press. This book was released on 1994-05-03 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a myriad of fresh ideas and energetic approaches to the newer aspects of everyday drug modelling. With contributions from some of the best young talents of today, Molecular Modelling and Drug Design encourages a break from old traditions and probes the unexplored avenues of the modelling tool. The contributors' views act as a gauge to future trends in computer-aided drug design-an area that continues to expand and play an ever more significant role in drug discovery.
Book Synopsis In Silico Medicinal Chemistry by : Nathan Brown
Download or read book In Silico Medicinal Chemistry written by Nathan Brown and published by Royal Society of Chemistry. This book was released on 2015-10-30 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering computational tools in drug design using techniques from chemoinformatics, molecular modelling and computational chemistry, this book explores these methodologies and applications of in silico medicinal chemistry. The first part of the book covers molecular representation methods in computing in terms of chemical structure, together with guides on common structure file formats. The second part examines commonly used classes of molecular descriptors. The third part provides a guide to statistical learning methods using chemical structure data, covering topics such as similarity searching, clustering and diversity selection, virtual library design, ligand docking and de novo design. The final part of the book summarises the application of methods to the different stages of drug discovery, from target ID, through hit finding and hit-to-lead, to lead optimisation. This book is a practical introduction to the subject for researchers new to the fields of chemoinformatics, molecular modelling and computational chemistry.
Book Synopsis Small Molecule Drug Discovery by : Andrea Trabocchi
Download or read book Small Molecule Drug Discovery written by Andrea Trabocchi and published by Elsevier. This book was released on 2019-11-23 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: Small Molecule Drug Discovery: Methods, Molecules and Applications presents the methods used to identify bioactive small molecules, synthetic strategies and techniques to produce novel chemical entities and small molecule libraries, chemoinformatics to characterize and enumerate chemical libraries, and screening methods, including biophysical techniques, virtual screening and phenotypic screening. The second part of the book gives an overview of privileged cyclic small molecules and major classes of natural product-derived small molecules, including carbohydrate-derived compounds, peptides and peptidomimetics, and alkaloid-inspired compounds. The last section comprises an exciting collection of selected case studies on drug discovery enabled by small molecules in the fields of cancer research, CNS diseases and infectious diseases. The discovery of novel molecular entities capable of specific interactions represents a significant challenge in early drug discovery. Small molecules are low molecular weight organic compounds that include natural products and metabolites, as well as drugs and other xenobiotics. When the biological target is well defined and understood, the rational design of small molecule ligands is possible. Alternatively, small molecule libraries are being used for unbiased assays for complex diseases where a target is unknown or multiple factors contribute to a disease pathology. - Outlines modern concepts and synthetic strategies underlying the building of small molecules and their chemical libraries useful for drug discovery - Provides modern biophysical methods to screening small molecule libraries, including high-throughput screening, small molecule microarrays, phenotypic screening and chemical genetics - Presents the most advanced chemoinformatics tools to characterize the structural features of small molecule libraries in terms of chemical diversity and complexity, also including the application of virtual screening approaches - Gives an overview of structural features and classification of natural product-derived small molecules, including carbohydrate derivatives, peptides and peptidomimetics, and alkaloid-inspired small molecules
Book Synopsis Molecular Interaction Fields by : Gabriele Cruciani
Download or read book Molecular Interaction Fields written by Gabriele Cruciani and published by John Wiley & Sons. This book was released on 2006-05-12 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique reference source, edited by the world's most respected expert on molecular interaction field software, covers all relevant principles of the GRID force field and its applications in medicinal chemistry. Entire chapters on 3D-QSAR, pharmacophore searches, docking studies, metabolism predictions and protein selectivity studies, among others, offer a concise overview of this emerging field. As an added bonus, this handbook includes a CD-ROM with the latest commercial versions of the GRID program and related software.
Book Synopsis Computational Drug Design by : D. C. Young
Download or read book Computational Drug Design written by D. C. Young and published by John Wiley & Sons. This book was released on 2009-01-28 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Helps you choose the right computational tools and techniques to meet your drug design goals Computational Drug Design covers all of the major computational drug design techniques in use today, focusing on the process that pharmaceutical chemists employ to design a new drug molecule. The discussions of which computational tools to use and when and how to use them are all based on typical pharmaceutical industry drug design processes. Following an introduction, the book is divided into three parts: Part One, The Drug Design Process, sets forth a variety of design processes suitable for a number of different drug development scenarios and drug targets. The author demonstrates how computational techniques are typically used during the design process, helping readers choose the best computational tools to meet their goals. Part Two, Computational Tools and Techniques, offers a series of chapters, each one dedicated to a single computational technique. Readers discover the strengths and weaknesses of each technique. Moreover, the book tabulates comparative accuracy studies, giving readers an unbiased comparison of all the available techniques. Part Three, Related Topics, addresses new, emerging, and complementary technologies, including bioinformatics, simulations at the cellular and organ level, synthesis route prediction, proteomics, and prodrug approaches. The book's accompanying CD-ROM, a special feature, offers graphics of the molecular structures and dynamic reactions discussed in the book as well as demos from computational drug design software companies. Computational Drug Design is ideal for both students and professionals in drug design, helping them choose and take full advantage of the best computational tools available. Note: CD-ROM/DVD and other supplementary materials are not included as part of eBook file.
Book Synopsis Molecular Diversity in Drug Design by : P.M. Dean
Download or read book Molecular Diversity in Drug Design written by P.M. Dean and published by Springer Science & Business Media. This book was released on 1999-10-31 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the theoretical problems associated with molecular diversity as it is being applied in the pharmaceutical industry. Therefore, this book deals with algorithms that are involved in understanding chemical space and selection of diverse sets of structures. The algorithms also deal with the problem of focused diversity where chemical libraries are being created within a structured physical volume. Diversity is necessarily connected to combinational chemistry, although this book is limited to the application of diversity methods to combinational chemistry and does not deal with synthetic methods. It is this focus on algorithms and strategies for exploiting molecular diversity that makes it different from books on combinational chemistry. The intended readership of the book falls into two categories: those actively engaged in applying molecular diversity in the chemical industry and those in academia who are developing strategies to embrace, understand and accept the many problems thrown up by this new research field of molecular diversity.
Book Synopsis Concepts and Applications of Molecular Similarity by : Mark A. Johnson
Download or read book Concepts and Applications of Molecular Similarity written by Mark A. Johnson and published by Wiley-Interscience. This book was released on 1990-09-24 with total page 420 pages. Available in PDF, EPUB and Kindle. Book excerpt: Offers authoritative overviews of topics related to the definition, computation and application of molecular similarity and emphasizes current research trends with molecular similarity as the unifying concept. Introduces and defines the concept of molecular similarity and explains how it can be used to explore the data containing 2-D and 3-D chemical information. Addresses the basic problem of relating chemical structures to their associated chemical and biological properties. Final chapters illustrate the use of similarity arguments in the study of chemical reaction pathways and present theoretical approaches to the concept of molecular similarity.
Book Synopsis Special Topics in Drug Discovery by : Taosheng Chen
Download or read book Special Topics in Drug Discovery written by Taosheng Chen and published by BoD – Books on Demand. This book was released on 2016-11-30 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drug discovery involves multiple disciplines, technologies, and approaches. This book selects important topics related to drug discovery, including emerging tool (Chapter 1), cutting-edge approaches (Chapters 2, 3, and 4), examples of specific therapeutic area (Chapter 5), quality control in drug development (Chapter 6), and job and career opportunities in the pharmaceutical sector, a topic rarely covered by other books (Chapter 7). This book draws knowledge from experts actively involved in different areas of drug discovery from both industrial and academic settings. We hope that this book will facilitate your efforts in drug discovery.
Book Synopsis Chemoinformatics Approaches to Virtual Screening by : Alexandre Varnek
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.
