Chemoinformatics and Computational Chemical Biology (Methods in Molecular Biology, 672)

Over the past years, the chem(o)informatics field has further evolved and new application areas have opened up, for example, in the broadly defined area of chemical biology. In Chemoinformatics and Computational Chemical Biology, leading investigators bring together a detailed series of reviews and methods including, among others, system-directed approaches using small molecules, the design of target-focused compound libraries, the study of molecular selectivity, and the systematic analysis of target-ligand interactions. Furthermore, the book delves into similarity methods, machine learning, probabilistic approaches, fragment-based methods, as well as topics that go beyond the current chemoinformatics spectrum, such as knowledge-based modeling of G protein-coupled receptor structures and computational design of siRNA libraries. As a volume in the highly successful Methods in Molecular BiologyTM series, this collection provides detailed descriptions and implementation advice that are exceedingly relevant for basic researchers and practitioners in this highly interdisciplinary research and development area. Cutting-edge and unambiguous, Chemoinformatics and Computational Chemical Biology serves as an ideal guide for experts and newcomers alike to this vital and dynamic field of study. Some trends in chem(o)informatics / Wendy A. Warr Molecular similarity measures / Gerald M. Maggiora and Veerabahu Shanmugasundaram The ups and downs of structure-activity landscapes / Rajarshi Guha Computational analysis of activity and selectivity cliffs / Lisa Peltason and Jürgen Bajorath Similarity searching using 2D structural fingerprints / Peter Willett Predicting the performance of fingerprint similarity searching / Martin Vogt and Jürgen Bajorath Bayesian methods in virtual screening and chemical biology / Andreas Bender Reduced graphs and their applications in chemoinformatics / Kristian Birchall and Valerie J. Gillet Fragment descriptors in structure-property modeling and virtual screening / Alexandre Varnek The scaffold tree : an efficient navigation in the scaffold universe / Peter Ertl, Ansgar Schuffenhauer, and Steffen Renner Pharmacophore-based virtual screening / Dragos Horvath De novo drug design / Markus Hartenfeller and Gisbert Schneider Classification of chemical reactions and chemoinformatics processing of enzymatic transformations / Diogo A.R.S. Latino and João Aires-de-Sousa Informatics approach to the rational design of siRNA libraries / Jerry O. Ebalunode, Charles Jagun, and Weifan Zheng Beyond rhodopsin : G protein-coupled receptor structure and modeling incorporating the [beta]2-adrenergic and adenosine A2a crystal structures / Andrew J. Tebben and Dora M. Schnur Methods for combinatorial and parallel library design / Dora M. Schnur, Brett R. Beno, Andrew J. Tebben, and Cullen Cavallaro The interweaving of cheminformatics and HTS / Anne Kümmel and Christian N. Parker Computational systems chemical biology / Tudor I. Oprea, Elebeoba E. May, Andrei Leitão, and Alexander Tropsha Ligand-based approaches to in silico pharmacology / David Vidal, Ricard Garcia-Serna, and Jordi Mestres Molecular test systems for cmputational selectivity studies and systematic analysis of compound selectivity profiles / Dagmar Stumpfe, Eugen Lounkine, and Jürgen Bajorath Application of support vector machine-based ranking strategies to search for target-selective compounds / Anne Mai Wassermann, Hanna Geppert, and Jürgen Bajorath What do we know? : simple statistical techniques that help / Anthony Nicholls. Front Matter....Pages i-x Back Matter....Pages 1-37 ....Pages 39-100