Unlike in the related area of bioinformatics, few books currently exist that document the techniques, tools, and algorithms of chemoinformatics. Bringing together worldwide experts in the field, the Handbook of Chemoinformatics Algorithms provides an overview of the most common chemoinformatics algorithms in a single source.
After a historical perspective of the applications of algorithms and graph theory to chemical problems, the book presents algorithms for two-dimensional chemical structures and three-dimensional representations of molecules. It then focuses on molecular descriptors, virtual screening methods, and quantitative structure–activity relationship (QSAR) models, before introducing algorithms to enumerate and sample chemical structures. The book also covers computer-aided molecular design, reaction network generation, and open source software and database technologies. The remaining chapters describe techniques developed in the context of bioinformatics and computational biology and their potential applications to chemical problems.
This handbook presents a selection of algorithms relevant in practice, making the book useful to those working in the field. It offers an up-to-date account of many algorithmic aspects of chemoinformatics.
Table of Contents
Representing 2D Chemical Structures with Molecular Graphs, Ovidiu Ivanciuc
Algorithms to Store and Retrieve 2D Chemical Structures, Milind Misra and Jean-Loup Faulon
3D Molecular Representations, Egon L. Willighagen
Molecular Descriptors, Nikolas Fechner, Georg Hinselmann, and Jörg Kurt Wegner
Ligand- and Structure-Based Virtual Screening, Robert D. Clark and Diana C. Roe
Predictive Quantitative Structure–Activity Relationships Modeling: Data Preparation and the General Modeling Workflow, Alexander Tropsha and Alexander Golbraikh
Predictive Quantitative Structure–Activity Relationships Modeling: Development and Validation of QSAR Models, Alexander Tropsha and Alexander Golbraikh
Structure Enumeration and Sampling, Markus Meringer
Computer-Aided Molecular Design: Inverse Design, Donald P. Visco, Jr.
Computer-Aided Molecular Design: De Novo Design, Diana C. Roe
Reaction Network Generation, Jean-Loup Faulon and Pablo Carbonell
Open Source Chemoinformatics Software and Database Technologies, Rajarshi Guha
Sequence Alignment Algorithms: Applications to Glycans, Trees, and Tree-Like Structures, Tatsuya Akutsu
Machine Learning-Based Bioinformatics Algorithms: Application to Chemicals, Shawn Martin
Using Systems Biology Techniques to Determine Metabolic Fluxes and Metabolite Pool Sizes, Fangping Mu, Amy L. Bauer, James R. Faeder, and William S. Hlavacek
Jean-Loup Faulon is a professor in the Department of Biology at the University of Evry in France.
Andreas Bender is an assistant professor in the Leiden/Amsterdam Center for Drug Research (LACDR) at Leiden University in the Netherlands.