An Introduction To Chemoinformatics

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.

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.

Von den Grundlagen zu Methoden - dieses Fachbuch, übersichtlich und didaktisch klar gegliedert, ist eine maßgebliche Handreichung mit allem Wissenswerten und Erläuterungen der Tools in diesem Fachgebiet.

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.

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.

More than 20 years of experience in molecular structure generation, from conceptualization through to applications Innovative, interdisciplinary text demonstrating example queries with software packages such as MOLGEN-online Detailed explanations on establishing QSPRs and QSARs as well as structure elucidation using mass spectrometry and structure generation. Aims and Scope This work provides an introduction to mathematical modeling of molecules and the resulting applications (structure generation, structure elucidation, QSAR/QSPR etc.). Most chemists have experimented with some software that represents molecules in an electronic form, and such models and applications are of increasing interest in diverse and growing fields such as drug discovery, environmental science and metabolomics. Furthermore, structure generation remains the only way to systematically create molecules that are not (yet) present in a database. This book starts with the mathematical theory behind representing molecules, explaining chemical concepts in mathematical terms and providing exercises that can be completed online. The later chapters cover applications of the theory, with detailed explanations on QSPR and QSAR investigations and finally structure elucidation combining mass spectrometry and structure generation. This book is aimed in particular at the users of structure generation methods and corresponding techniques, but also for those interested in teaching and learning mathematical chemistry, and for software designers in chemoinformatics.

Introduction to Computational Chemistry 3rd Edition provides a comprehensive account of the fundamental principles underlying different computational methods. Fully revised and updated throughout to reflect important method developments and improvements since publication of the previous edition, this timely update includes the following significant revisions and new topics: Polarizable force fields Tight-binding DFT More extensive DFT functionals, excited states and time dependent molecular properties Accelerated Molecular Dynamics methods Tensor decomposition methods Cluster analysis Reduced scaling and reduced prefactor methods Additional information is available at: www.wiley.com/go/jensen/computationalchemistry3

30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies. Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website. Key topics and methods covered in Tutorials in Chemoinformatics include: Data curation and standardization Development and use of chemical databases Structure encoding by molecular descriptors, text strings and binary fingerprints The design of diverse and focused libraries Chemical data analysis and visualization Structure-property/activity modeling (QSAR/QSPR) Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces 3D pharmacophores modeling and pharmacological profiling using shape analysis Protein-ligand docking Implementation of algorithms in a high-level programming language Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills.

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.