Table of Contents

Contributors vii

Foreword xi

Preface xvii

1 Bridging Chemical and Biological Information: Public Knowledge Spaces 1
Paul A. Thiessen, Wolf-D. Ihlenfeldt, Evan E. Bolton, and Stephen H. Bryant

2 Bridging Chemical and Biological Data: Implications for Pharmaceutical Drug Discovery 25
Jeremy L. Jenkins, Josef Scheiber, Dmitri Mikhailov, Andreas Bender, Ansgar Schuffenhauer, Ben Cornett, Vivien Chan, Jason Kondracki, Bernhard Rohde, and John W. Davies

3 Chemoinformatics Taking Biology Into Account: Proteochemometrics 57
Jarl E. S. Wikberg, Ola Spjuth, Martin Eklund, and Maris Lapins

4 Compound Activities in Times of Systems Biology 93
David E. Patterson

5 Molecular Descriptors for Biological Systems 107
N. Sukumar, Sourav Das, Michael Krein, Rahul Godawat, Inna Vitol, Shekhar Garde, Kristin P. Bennett, and Curt M. Breneman

6 Graphs: Flexible Representations of Molecular Structures and Biological Networks 145
Milind Misra, Shawn Martin, and Jean-Loup Faulon

7 Workflow Tools for Managing Biological and Chemical Data 179
Thorsten Meinl, Bernd Wiswedel, and Michael R. Berthold

8 Using Chemical Structure to Infer Biological Function 211
Angelo D. Favia and Irene Nobeli

9 Using Chemical Structure as Probes for Biological Networks 239
Florian Nigsch

Index 261

About the Author

RAJARSHI GUHA, PhD, is a Research Scientist at the NIH Center for Translational Therapeutics in Rockville, Maryland. His research covers a variety of topics in cheminformatics and chemical data mining, addressing software and methodology development as well as applications in areas such as high throughput screening and high content imaging of small molecules and siRNA's. Prior to working at the NIH, he was a visiting assistant professor in the School of Informatics and Computing, Indiana University.

ANDREAS BENDER, PhD, is a Lecturer for Molecular Informatics with the Unilever Centre for Molecular Science Informatics at the University of Cambridge. His research encompasses ways to integrate—and analyze—chemical, biological, and phenotypic data, with the aim to design molecular structures with a desired property profile. Andreas Bender received his PhD from the University of Cambridge and worked for the Novartis Institutes for Biomedical Research in Cambridge, Massachusetts before returning to his current position in academia.