An open-source software package for creating and operating web-based structure and/or reaction databases is presented. Besides standard search capabilities (text, structure/substructure/similarity), the system offers a fast additional search option, entirely based on binary pattern matching, which uses automatically assigned functional group descriptors.

A novel chemical ontology based on chemical functional groups automatically, objectively assigned by a computer program, was developed to categorize small molecules. It has been applied to PubChem and the small molecule interaction database to demonstrate its utility as a basic pharmacophore search system. Molecules can be compared using a semantic similarity score based on functional group assignments rather than 3D shape, which succeeds in identifying small molecules known to bind a common binding site. This ontology will serve as a powerful tool for searching chemical databases and identifying key functional groups responsible for biological activities.

SSAO/VAP-1 is not only involved in the metabolism of biogenic and xenobiotic primary amines and in the production of metabolites with cytotoxic effects or certain physiological actions, but also plays a role, for example, as an adhesion molecule, in leukocyte trafficking, in regulating glucose uptake and in adipocyte homeostasis. Interest in the enzyme has been stimulated by the findings that the activities of the SSAOs are altered (mostly increased) in various human disorders, including diabetes, congestive heart failure, liver cirrhosis, Alzheimer's disease and several inflammatory diseases, although the underlying causes are often unknown. On the basis of their insulin-mimicking effect, SSAO substrates are possibly capable of ameliorating metabolic changes in diabetes, while SSAO inhibitors (somewhat of a contradiction) are of potential benefit in preventing diabetes complications, atherosclerosis and oxidative stress contributing to several disorders or modulating inflammation, and hence may be of substantial therapeutic value. Great efforts have been made to develop novel compounds which may lead to future drugs useful in therapy, based on their effects on SSAO/VAP-1, and some of the results relating to novel substrates and inhibitors are surveyed in the present review.

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Abstract:The article describes a classification system termed "extended functional groups" (EFG), which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts) of the On-line CHEmical database and Modeling (OCHEM) environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models.