ReactionCode: format for reaction searching, analysis, classification, transform, and encoding/decoding.

In the past two decades a lot of different formats for molecules and reactions have been created. These formats were mostly developed for the purposes of identifiers, representation, classification, analysis and data exchange. A lot of efforts have been made on molecule formats but only few for reactions where the endeavors have been made mostly by companies leading to proprietary formats.

SAVI, in silico generation of billions of easily synthesizable compounds through expert-system type rules.

We have made available a database of over 1 billion compounds predicted to be easily synthesizable, called Synthetically Accessible Virtual Inventory (SAVI). They have been created by a set of transforms based on an adaptation and extension of the CHMTRN/PATRAN programming languages describing chemical synthesis expert knowledge, which originally stem from the LHASA project. The chemoinformatics toolkit CACTVS was used to apply a total of 53 transforms to about 150,000 readily available building blocks (enamine.

Adapting CHMTRN (CHeMistry TRaNslator) for a New Use.

We have adopted and extended the CHMTRN language and used it for the knowledge base of a computer program to generate a large database of synthetically accessible, drug-like chemical structures, the Synthetically Accessible Virtual Inventory (SAVI) Database. CHMTRN is a powerful language originally developed in the LHASA (Logic and Heuristics Applied to Synthetic Analysis) project at Harvard University and used together with the chemical pattern description language, PATRAN, to describe chemical retro-reactions. The languages have proven to be useful beyond the design of retrosynthetic routes and have the potential for much wider use in chemistry; this paper describes CHMTRN and PATRAN as now reimplemented for the forward-synthetic SAVI project but able to describe both forward and retro-reactions.

Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2.

We have collected 86 different transforms of tautomeric interconversions. Out of those, 54 are for prototropic (non-ring-chain) tautomerism, 21 for ring-chain tautomerism, and 11 for valence tautomerism. The majority of these rules have been extracted from experimental literature.

In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans.

Heterocyclic Aromatic Amines (HAAs) are environmental and food contaminants that are classified as probable or possible carcinogens by the International Agency for Research on Cancer. Thirty different HAAs have been identified. However the metabolism of only three of them have been fully characterized in human hepatocytes: AαC (2-amino-9H-pyrido[2,3-b]indole), MeIQx (2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline) and PhIP (2-amino-1-methyl-6-phenyl-imidazo[4,5-b]pyridine).

A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes.

Background: Heterocyclic aromatic amines (HAA) are environmental and food contaminants that are potentially carcinogenic for humans. 2-Amino-3,8-dimethylimidazo[4,5-]quinoxaline (MeIQx) is one of the most abundant HAA formed in cooked meat. MeIQx is metabolized by cytochrome P450 1A2 in the human liver into detoxificated and bioactivated products.