Recent advances in chemoinformatics.

Chemoinformatics is a large scientific discipline that deals with the storage, organization, management, retrieval, analysis, dissemination, visualization, and use of chemical information. Chemoinformatics techniques are used extensively in drug discovery and development. Although many consider it a mature field, the advent of high-throughput experimental techniques and the need to analyze very large data sets have brought new life and challenges to it. Here, we review a selection of papers published in 2006 that caught our attention with regard to the novelty of the methodology that was presented. The field is seeing significant growth, which will be further catalyzed by the widespread availability of public databases to support the development and validation of new approaches.

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[72]  Hui Xiong,et al.  Hyperclique pattern discovery , 2006, Data Mining and Knowledge Discovery.

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[75]  Takashi Washio,et al.  Applying the Apriori-based Graph Mining Method to Mutagenesis Data Analysis , 2001 .

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[80]  Stefan Wetzel,et al.  The Scaffold Tree - Visualization of the Scaffold Universe by Hierarchical Scaffold Classification , 2007, J. Chem. Inf. Model..

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[87]  Lydia E Kavraki,et al.  Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.

[88]  Mihaly Mezei,et al.  Morphology of Voids in Molecular Systems. A Voronoi−Delaunay Analysis of a Simulated DMPC Membrane , 2004 .

[89]  Dimitris K. Agrafiotis,et al.  A distance geometry heuristic for expanding the range of geometries sampled during conformational search , 2006, J. Comput. Chem..

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[91]  Luc De Raedt,et al.  Data Mining and Machine Learning Techniques for the Identification of Mutagenicity Inducing Substructures and Structure Activity Relationships of Noncongeneric Compounds , 2004, J. Chem. Inf. Model..

[92]  Claudio Chuaqui,et al.  Structural Interaction Fingerprints: A New Approach to Organizing, Mining, Analyzing, and Designing Protein–Small Molecule Complexes , 2006, Chemical biology & drug design.

[93]  Thorsten Meinl,et al.  Hybrid fragment mining with MoFa and FSG , 2004, 2004 IEEE International Conference on Systems, Man and Cybernetics (IEEE Cat. No.04CH37583).

[94]  Monya Baker,et al.  Open-access chemistry databases evolving slowly but not surely , 2006, Nature Reviews Drug Discovery.

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[96]  Alexander Tropsha,et al.  Simplicial neighborhood analysis of protein packing (SNAPP): a computational geometry approach to studying proteins. , 2003, Methods in enzymology.

[97]  Paolo Mazzatorta,et al.  Integration of Structure-Activity Relationship and Artificial Intelligence Systems To Improve in Silico Prediction of Ames Test Mutagenicity , 2007, J. Chem. Inf. Model..

[98]  Roger A. Sayle,et al.  Electrostatic evaluation of isosteric analogues , 2006, J. Comput. Aided Mol. Des..

[99]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[100]  Thomas Bäck,et al.  Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés" , 2006, J. Chem. Inf. Model..