- Elisabet Gregori-Puigjané, Jordi Mestres. SHED: Shannon Entropy Descriptors from Topological Feature Distributions. Journal of Chemical Information and Computer Sciences, 46(4):1615-1622, 2006.
- Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer. Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. Journal of Chemical Information and Computer Sciences, 46(2):903-911, 2006.
- Modest von Korff, Kurt Hilpert. Assessing the Predictive Power of Unsupervised Visualization Techniques to Improve the Identification of GPCR-Focused Compound Libraries. Journal of Chemical Information and Computer Sciences, 46(4):1580-1587, 2006.
- Samuel Toba, Jayashree Srinivasan, Allister J. Maynard, Jon M. Sutter. Using Pharmacophore Models To Gain Insight into Structural Binding and Virtual Screening: An Application Study with CDK2 and Human DHFR. Journal of Chemical Information and Computer Sciences, 46(2):728-735, 2006.
- Igor V. Tetko, Vitaly P. Solov ev, Alexey V. Antonov, Xiaojun Yao, Jean-Pierre Doucet, Bo Tao Fan, Frank Hoonakker, Denis Fourches, Piere Jost, Nicolas Lachiche, Alexandre Varnek. Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores. Journal of Chemical Information and Computer Sciences, 46(2):808-819, 2006.
- Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman. Mining a Chemical Database for Fragment Co-occurrence: Discovery of Chemical Clichés . Journal of Chemical Information and Computer Sciences, 46(2):553-562, 2006.
- Alireza Givehchi, Andreas Bender, Robert C. Glen. Analysis of Activity Space by Fragment Fingerprints, 2D Descriptors, and Multitarget Dependent Transformation of 2D Descriptors. Journal of Chemical Information and Computer Sciences, 46(3):1078-1083, 2006.
- Sara H. Fitzgerald, Michal Sabat, H. Mario Geysen. Diversity Space and Its Application to Library Selection and Design. Journal of Chemical Information and Computer Sciences, 46(4):1588-1597, 2006.
- Chidochangu P. Mpamhanga, Beining Chen, Iain M. McLay, Peter Willett 0002. Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions. Journal of Chemical Information and Computer Sciences, 46(2):686-698, 2006.
- Nicola D. Gold, Richard M. Jackson. A Searchable Database for Comparing Protein-Ligand Binding Sites for the Analysis of Structure-Function Relationships. Journal of Chemical Information and Computer Sciences, 46(2):736-742, 2006.