The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.

In this paper we illustrate the application of the ISIDA (In SIlico design and Data Analysis) software to perform virtual screening of large databases of compounds and reactions and to assess some ADME/Tox properties. ISIDA represents an ensemble of tools allowing users to store, search and analyze the data, to perform similarity searches in large databases of molecules and reactions, to build and validate QSAR models, and to generate and screen virtual combinatorial libraries. It uses its own descriptors (substructural molecular fragments and fuzzy pharmacophore triplets). Workflow can be easily organized by combining different ISIDA modules. Several examples of ISIDA applications (similarity search of potent benzodiazepine ligands with FPT, QSAR modeling of aqueous solubility, aquatic toxicity, tissue-air partition coefficients, anti-HIV activity, and screening of the “Chimiotheque Nationale” Database), are discussed. Particular attention is paid to mining reaction databases using Condensed Reaction Graphs approach.