An Introduction to Chemoinformatics

Author: Andrew R. Leach
Publisher: Springer Science & Business Media
ISBN: 9781402062902
Format: PDF, Mobi
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Chemoinformatics draws upon techniques from many disciplines including computer science, mathematics, computational chemistry and data visualisation. This text aims to provide an introduction to the major techniques of chemoinformatics.

Chemoinformatics

Author: Jürgen Bajorath
Publisher: Springer Science & Business Media
ISBN: 1592598021
Format: PDF, ePub
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Well-recognized pioneers and investigators from diverse professional environments survey the key concepts in the field, describe cutting-edge methods, and provide exemplary pharmaceutical applications. The authors explain the theory behind the crucial concepts of molecular similarity and diversity, describe the challenging efforts to use chemoinformatics approaches to virtual and high-throughput screening, and illuminate the latest developments in multidimensional QSAR analysis. Other topics of interest include the use of partitioning algorithms and classification methods for analyzing large compound databases, screening sets, and virtual screening for active molecules; different approaches to target class-specific library design; and the generation of a novel class of molecular surface properties descriptors that can be readily calculated from 2D representations of molecular structures. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery illuminates the conceptual and methodological diversity of this rapidly evolving field and offers instructive examples of cutting-edge applications in the drug discovery process. Understand the key concepts and novel methods behind chemoinformatics See cutting-edge chemoinformatic methods applied to the drug discovery process Appreciate the conceptual and methodological diversity of chemoinformatics Master the basics of machine learning, library design, and ADME modeling.

Chemoinformatics

Author: Johann Gasteiger
Publisher: John Wiley & Sons
ISBN: 3527606505
Format: PDF, ePub
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This first work to be devoted entirely to this increasingly important field, the "Textbook" provides both an in-depth and comprehensive overview of this exciting new area. Edited by Johann Gasteiger and Thomas Engel, the book provides an introduction to the representation of molecular structures and reactions, data types and databases/data sources, search methods, methods for data analysis as well as such applications as structure elucidation, reaction simulation, synthesis planning and drug design. A "hands-on" approach with step-by-step tutorials and detailed descriptions of software tools and Internet resources allows easy access for newcomers, advanced users and lecturers alike. For a more detailed presentation, users are referred to the "Handbook of Chemoinformatics", which will be published separately. Johann Gasteiger is the recipient of the 1991 Gmelin-Beilstein Medal of the German Chemical Society for Achievements in Computer Chemistry, and the Herman Skolnik Award of the Division of Chemical Information of the American Chemical Society (ACS) in 1997. Thomas Engel joined the research group headed by Johann Gasteiger at the University of Erlangen-Nuremberg and is a specialist in chemoinformatics.

Chemoinformatics in Drug Discovery

Author: Tudor I. Oprea
Publisher: John Wiley & Sons
ISBN: 3527604200
Format: PDF, ePub, Docs
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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.

Chemometrics and chemoinformatics

Author: Barry K. Lavine
Publisher: An American Chemical Society Publication
ISBN:
Format: PDF, Docs
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Chemometrics and Chemoinformatics gives chemists and other scientists an introduction to the field of chemometrics and chemoinformatics. Chemometrics is an approach to analytical chemistry based on the idea of indirect observation. Measurements related to the chemical composition of a substance are taken, and the value of a property of interest is inferred from them through some mathematical relation. Basically, chemometrics is a process. Measurements are made, data is collected, and information is obtained to periodically assess and acquire knowledge. This, in turn, has led to a new approach for solving scientific problems: (1) measure a phenomenon or process using chemical instrumentation that generates data inexpensively, 92) analyze the multivariate data, (3) iterate if necessary, (4) create and test the model, and (5) develop fundamental multivariate understanding of the process. Chemoinformatics is a subfield of chemometrics, which encompasses the analysis, visualization, and use of chemical structural information as a surrogate variable for other data or information. The boundaries of chemoinformatics have not yet been defined. Only rcently has this term been coined. Chemoinformatics takes advantage of techniques from many disciplines such as molecular modeling, chemical information, and computational chemistry. The reason for the interest in chemoinformatics is the development of experimental techniques such as combinatorial chemistry and high-throughput screening, which require a chemist to analyze unprecedented volumes of data. Access to appropriate algorithms is crucial if such experimental techniques are to be effectively exploited for discovery. Many chemisty want to use chemoinformatic methods in their work but lack the knowledge to decide what techniques are the most appropriate.

Chemoinformatics

Author: Hossein G. Gilani
Publisher: CRC Press
ISBN: 1926895231
Format: PDF, Docs
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Chemoinformatics: Advanced Control and Computational Techniques provides an important understanding of the main computational techniques used for processing chemical and biological structural data. The theoretical background to a number of techniques is introduced. General data analysis techniques and examination of the application techniques in the industy are presented, along with current practices and current research. The book also provides practical experience of commercially available systems and includes small-scale chemoinformatics-related projects. The book offers scope for academics, researchers, and engineering professionals. Chapters range from new methods to novel applications of existing methods and help provide an understanding of the material and/or structural behavior of new and advanced systems. It includes innovative chapters on the growth of educational, scientific, and industrial research activities among chemical engineers. It provides the latest coverage of chemical databases and the development of new computational methods and efficient algorithms for chemical software and chemical engineering.

Mathematical Chemistry and Chemoinformatics

Author: Adalbert Kerber
Publisher: Walter de Gruyter
ISBN: 3110254077
Format: PDF, Docs
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This work provides an introduction to mathematical modeling of molecules and its applications (structure generation, elucidation, evaluation; QSAR/QSPR etc.). It contains exercises and explanations of software packages in chemoinformatics that can be used directly via an online login code. It is aimed at users of structure generation and corresponding methods, but also for teaching and learning chemoinformatics and for software designers.

Chemoinformatics

Author: Thomas Engel
Publisher: John Wiley & Sons
ISBN: 3527693777
Format: PDF
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This essential guide to the knowledge and tools in the field includes everything from the basic concepts to modern methods, while also forming a bridge to bioinformatics. The textbook offers a very clear and didactical structure, starting from the basics and the theory, before going on to provide an overview of the methods. Learning is now even easier thanks to exercises at the end of each section or chapter. Software tools are explained in detail, so that the students not only learn the necessary theoretical background, but also how to use the different software packages available. The wide range of applications is presented in the corresponding book Applied Chemoinformatics - Achievements and Future Opportunities (ISBN 9783527342013). For Master and PhD students in chemistry, biochemistry and computer science, as well as providing an excellent introduction for other newcomers to the field.

Practical Chemoinformatics

Author: Muthukumarasamy Karthikeyan
Publisher: Springer
ISBN: 8132217802
Format: PDF, Mobi
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Chemoinformatics is equipped to impact our life in a big way mainly in the fields of chemical, medical and material sciences. This book is a product of several years of experience and passion for the subject written in a simple lucid style to attract the interest of the student community who wish to master chemoinformatics as a career. The topics chosen cover the entire spectrum of chemoinformatics activities (methods, data and tools). The algorithms, open source databases, tutorials supporting theory using standard datasets, guidelines, questions and do it yourself exercises will make it valuable to the academic research community. At the same time every chapter devotes a section on development of new software tools relevant for the growing pharmaceutical, fine chemicals and life sciences industry. The book is intended to assist beginners to hone their skills and also constitute an interesting reading for the experts.

Chemoinformatics Approaches to Virtual Screening

Author: Alexandre Varnek
Publisher: Royal Society of Chemistry
ISBN: 0854041443
Format: PDF, Mobi
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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.