Chemoinformatics for Drug Discovery

JÜRGEN BAJORATH, PhD, is Chair of Life Science Informatics at the University of Bonn and also an Affiliate Professor in the Department of Biological Structure at the University of Washington. In addition, he has more than 10 years' experience in drug disovery. His research focuses on the development of computational methods for medicinal chemistry and chemical biology. Dr. Bajorath holds 26 patents, has authored more than 400 scientific articles, and edited four books.

• Preface viiContributors xiii1 What Are Our Models Really Telling Us? A Practical Tutorial on Avoiding Common Mistakes when Building Predictive Models 1W. Patrick Walters2 The Challenge of Creativity in Drug Design 33Ajay N. Jain3 A Rough Set Theory Approach to the Analysis of Gene Expression Profiles 51Joachim Petit, Nathalie Meurice, José Luis Medina-Franco, and Gerald M. Maggiora4 Bimodal Partial Least-Squares Approach and Its Application to Chemogenomics Studies for Molecular Design 85Kiyoshi Hasegawa and Kimito Funatsu5 Stability in Molecular Fingerprint Comparison 97Anthony Nicholls and Brian Kelley6 Critical Assessment of Virtual Screening for Hit Identification 113Dagmar Stumpfe and Jürgen Bajorath7 Chemometric Applications of Naïve Bayesian Models in Drug Discovery: Beyond Compound Ranking 131Eugen Lounkine, Peter S. Kutchukian, and Meir Glick8 Chemoinformatics in Lead Optimization 149Darren V. S. Green and Matthew Segall9 Using Chemoinformatics Tools to Analyze Chemical Arrays in Lead Optimization 179George Papadatos, Valerie J. Gillet, Christopher N. Luscombe, Iain M. McLay, Stephen D. Pickett, and Peter Willett10 Exploration of Structure–Activity Relationships (SARs) and Transfer of Key Elements in Lead Optimization 205Hans Matter, Stefan Güssregen, Friedemann Schmidt, Gerhard Hessler, Thorsten Naumann, and Karl-Heinz Baringhaus11 Development and Applications of Global ADMET Models: In Silico Prediction of Human Microsomal Lability 245Karl-Heinz Baringhaus, Gerhard Hessler, Hans Matter, and Friedemann Schmidt12 Chemoinformatics and Beyond: Moving from Simple Models to Complex Relationships in Pharmaceutical Computational Toxicology 267Catrin Hasselgren, Daniel Muthas, Ernst Ahlberg, Samuel Andersson, Lars Carlsson, Tobias Noeske, Jonna Stålring, and Scott Boyer13 Applications of Cheminformatics in Pharmaceutical Research: Experiences at Boehringer Ingelheim in Germany 291Bernd Beck, Michael Bieler, Peter Haebel, Andreas Teckentrup, Alexander Weber, and Nils Weskamp14 Lessons Learned from 30 Years of Developing Successful Integrated Cheminformatic Systems 321Michael S. Lajiness and Thomas R. Hagadone15 Molecular Similarity Analysis 343José L. Medina-Franco and Gerald M. MaggioraIndex 401

“Overall the book is well written, logically following the larger storyline and most of the time offering high quality reviews . . . Personally, I enjoyed reading this book and would recommend it as a general introduction to the subject aimed especially for post-graduate students and non-specialists working in the area of drug design, but also for all of those who just want to update their knowledge.”  (ChemMedChem, 1 June 2014)