Tutorials in Chemoinformatics

Author: Alexandre Varnek

Publisher: John Wiley & Sons

ISBN: 1119137985

Category: Science

Page: 488

View: 2166

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.


Basic Concepts and Methods

Author: Thomas Engel,Johann Gasteiger

Publisher: John Wiley & Sons

ISBN: 3527693785

Category: Science

Page: 600

View: 8045

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,Renu Vyas

Publisher: Springer

ISBN: 8132217802

Category: Science

Page: 533

View: 2440

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.


A Textbook

Author: Johann Gasteiger,Thomas Engel

Publisher: John Wiley & Sons

ISBN: 3527606505

Category: Science

Page: 680

View: 1594

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.

Chemometrics and chemoinformatics

Author: Barry K. Lavine,American Chemical Society. Division of Computers in Chemistry,American Chemical Society. Meeting

Publisher: An American Chemical Society Publication


Category: Science

Page: 204

View: 2789

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 for Drug Discovery

Author: Jürgen Bajorath

Publisher: John Wiley & Sons

ISBN: 1118743091

Category: Science

Page: 432

View: 5877

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.

Molecular Descriptors for Chemoinformatics

Volume I: Alphabetical Listing / Volume II: Appendices, References

Author: Roberto Todeschini,Viviana Consonni,Raimund Mannhold

Publisher: Wiley-VCH Verlag GmbH

ISBN: 9783527318520

Category: Medical

Page: 1257

View: 9818

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.

Adaptive Systems in Drug Design

Author: Gisbert Schneider,Sung-Sau So

Publisher: CRC Press


Category: Medical

Page: 173

View: 1729

A brief history of drug design presented to make clear that there are fashions in this important field and that they change rather rapidly. This is due in part to the fact that the way that a new paradigm is accepted in a drug company often does not depend on its scientific merit alone.

Research by design

innovation and T.C.S.

Author: Shivanand Kanavi

Publisher: N.A


Category: Technological innovations

Page: 336

View: 425

Der HPLC-Experte

Möglichkeiten und Grenzen der modernen HPLC

Author: Stavros Kromidas

Publisher: John Wiley & Sons

ISBN: 3527676589

Category: Science

Page: 446

View: 3776

Der rasanten Entwicklung auf dem Gebiet der HPLC wird mit diesem Buch Rechnung getragen: Von Gradientenoptimierung über Kopplungs- und 2D-Techniken bis zu Dokumentation und Informationsbeschaffung - aktuell und kompakt geschrieben von Praktikern für Praktiker. Inhalt: 1 LC/MS-Kopplung 1.1 Stand der Technik in der LC/MS-Kopplung 1.2 Technische Aspekte und Fallstricke der LC/MS-Kopplung 1.3 LC/MS-Kopplung - ein praktisches Beispiel aus der Ionenchromatographie 2 HPLC-GC-Kopplung in der Praxis; Theorie, Applikationsbeispiele und Ausblick 3 Optimisierungsstrategien in der RP-HPLC 4 Der Gradient in der RP-Chromatographie 4.1 Aspekte der Gradienten-Optimierung 4.2 Vorhersagen von Gradienten 5 Vergleich und Auswahl von modernen HPLC-Säulen 6 Trenntechniken in der Biochromatographie 7 Moderne HPLC-Softwareprogramme - Eigenschaften, Vergleich, Ausblick 8 Möglichkeiten der "richtigen" Integration heute 9 HPLC im reglementierten Bereich 9.1 Intelligente Dokumentationen 9.2 Tipps für eine gelungene FDA-Inspektion 10 Effiziente Informationsbeschaffung im Zeitalter von Web 2.0 am Beispiel der HPLC 11 Trends in der Detektionstechnik

Molekülorbitale und Reaktionen organischer Verbindungen

Author: Ian Fleming

Publisher: John Wiley & Sons

ISBN: 3527330690

Category: Chemical bonds

Page: 399

View: 4683

Der lang erwartete Nachfolger des Klassikers "Grenzorbitale und Reaktionen organischer Verbindungen". Die Molekülorbitalheorie wird einfach, ohne komplizierte mathematische Formeln und mit vielen illustrativen Beispielen erklärt.

Data mining

praktische Werkzeuge und Techniken für das maschinelle Lernen

Author: Ian H. Witten,Eibe Frank

Publisher: N.A

ISBN: 9783446215337


Page: 386

View: 5984


Ein Lehrbuch

Author: Jürgen H Gross

Publisher: Springer-Verlag

ISBN: 3827429811

Category: Science

Page: 802

View: 5939

Mit Massenspektrometrie – ein Lehrbuch liegt ein Werk vor, das mit seiner umfassenden, präzisen Darstellung sowie seinen vielen gelungenen Illustrationen und Fotos eine Lücke auf dem deutschsprachigen Markt schließt. Dieses im englischsprachigen Raum bereits gut etablierte Buch führt auf grundlegende Weise an die Massenspektrometrie heran, indem es die Prinzipien, Methoden und Anwendungen logisch aufeinander aufbauend erklärt. Schritt für Schritt lernt der Leser, was diese analytische Methode leisten kann, auf welch vielfältige Art Massenspektrometer isolierte Ionen in der Gasphase erzeugen, selektieren und manipulieren können und wie man aus den resultierenden Massenspektren analytische Information gewinnt. Moderne sanfte Ionisationsmethoden wie ESI, APCI oder MALDI, klassische Verfahren wie EI, CI, FAB oder FD, Oberflächentechniken wie DESI oder DART und elementmassenspektrometrische Verfahren werden didaktisch durchdacht behandelt. Studienanfänger werden von dem Werk ebenso profitieren wie Fortgeschrittene und Praktiker. Ergänzend zum Buch betreibt der Autor eine frei zugängliche (englischsprachige) Internetseite mit zahlreichen Übungsaufgaben, Lösungen und Bonus-Material unter http://www.ms-textbook.com