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.
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.
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.
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.
Publisher: An American Chemical Society Publication
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.
As every chemist knows, there is a direct (if complex) relationship between the molecular structure of a compound and its chemical behavior. Predicting such behavior is possible by an abstract representation of its structure in terms of chemical similarity parameters, so-called 'descriptors'. These are most useful in predicting the pharmacological properties of drug candidates, but are also used in predicting reactivity, toxicity and other important chemical characteristics. The number-one reference on the topic now contains a wealth of new data: The entire relevant literature over the past six years has been painstakingly surveyed, resulting in more than 100 new descriptors being added to the list, and some 3,000 new references in the bibliography section. Volume 1 contains an alphabetical listing of around 3300 terms for the chemoinformatic analysis of chemical compound properties, while the second volume contains 6343 references selected from 450 journals with about 7000 authors quoted covering the period from the beginning of molecular descriptor research until the year 2008. In this second edition, the greatly expanded introductory section has been completely re-written and now contains several "walk-through" reading lists of selected keywords to make the data even more accessible for novice users.
Chemoinformatics strategies to improve drug discoveryresults With contributions from leading researchers in academia and thepharmaceutical industry as well as experts from the softwareindustry, this book explains how chemoinformatics enhances drugdiscovery and pharmaceutical research efforts, describing whatworks and what doesn't. Strong emphasis is put on tested and provenpractical applications, with plenty of case studies detailing thedevelopment and implementation of chemoinformatics methods tosupport successful drug discovery efforts. Many of these casestudies depict groundbreaking collaborations between academia andthe pharmaceutical industry. Chemoinformatics for Drug Discovery is logicallyorganized, offering readers a solid base in methods and models andadvancing to drug discovery applications and the design ofchemoinformatics infrastructures. The book features 15 chapters,including: What are our models really telling us? A practical tutorial onavoiding common mistakes when building predictive models Exploration of structure-activity relationships and transfer ofkey elements in lead optimization Collaborations between academia and pharma Applications of chemoinformatics in pharmaceuticalresearch—experiences at large international pharmaceuticalcompanies Lessons learned from 30 years of developing successfulintegrated chemoinformatic systems Throughout the book, the authors present chemoinformaticsstrategies and methods that have been proven to work inpharmaceutical research, offering insights culled from their owninvestigations. Each chapter is extensively referenced withcitations to original research reports and reviews. Integrating chemistry, computer science, and drug discovery,Chemoinformatics for Drug Discovery encapsulates the fieldas it stands today and opens the door to further advances.