Reaction Libraries
CTS Reaction Libraries are composed of generalized reaction schemes that that specify how a molecular fragment will be modified by a particular transformation process (e.g., abiotic hydrolysis, abiotic reduction, and mammalian metabolism). The reaction schemes were developed based on reported transformation pathways and products from the peer-reviewed literature and regulatory reports. The reaction libraries are considered to be comprehensive based on review of the current literature; however, updates will be made as additional studies are published.
Prediction of Transformation Pathways
When a user submits a molecule of interest in the CTS Generate Transformation Products workflow, CTS compares the molecule to the reactant side of each scheme within the Reaction Library. If CTS finds a match between a structural fragment within the molecule and the reactant side of a scheme, it modifies the fragment according to the scheme, leaving the rest of the molecule unchanged. Because a molecule may contain multiple structural fragments that match the reactant side of different reaction schemes, multiple products can be generated from the parent molecule. To predict which of these products are the most likely to accumulate, CTS calculates the "production" and "accumulation" of each product using an integer rank that has been assigned to each reaction scheme within the CTS Reaction Libraries based on reported transformation rates in the scientific literature.
Algorithm for Prediction of Likely Transformation Products
Abiotic Hydrolysis Reaction Library
The current version of the Abiotic Hydrolysis Reaction Library contains 24 reaction schemes. In the documentation page, left click a reaction scheme to view the generalized reaction scheme, supporting reaction rules for reactivity, selectivity and exclusion, as well as example transformation pathways and associated references. Scroll to the bottom of the library documentation page to view a table showing the rank assignments for each scheme in the library.
Abiotic Hydrolysis Reaction Library (last updated September 11, 2020)
Abiotic Reduction Reaction Library
The current version of the Abiotic Reduction Reaction Library contains eight reaction schemes. In the documentation page, left click a reaction scheme to view the generalized reaction scheme, supporting reaction rules for reactivity, selectivity and exclusion, as well as example transformation pathways and associated references. Scroll to the bottom of the library documentation page to view a table showing the rank assignments for each scheme in the library.
Abiotic Reduction Reaction Library (last updated August 6, 2020)
Direct Photolysis Reaction Library
There are currently 154 reaction schemes in the Direct Photolysis Reaction Library. There are ranked and unranked versions of the library. The unranked library generates all possible phototransformation products and should not be run with other libraries. In the documentation pages for the ranked and unranked libraries, left click a reaction scheme to view the generalized reaction scheme, supporting reaction rules for reactivity, selectivity and exclusion, as well as example transformation pathways and associated references. Scroll to the bottom of the ranked library documentation page to view a table showing the rank assignments for each scheme in the library.
Direct Photolysis Reaction Library (unranked) (last updated April 21, 2020)
Direct Photolysis Reaction Library (ranked) (last updated April 30, 2021)
Spontaneous Reaction Library
The Spontaneous Reaction Library contains aqueous reactions that occur very quickly and is intended to be combined with other CTS reaction libraries. It was developed to capture the rapid transformation of intermediates that form due to other transformation processes (e.g., hydrolysis or photolysis). The current version of Spontaneous Reaction Library contains one reaction scheme.
Spontaneous Reaction Library (last updated July 7, 2020)
Human Phase 1 Metabolism Reaction Library
The Human Phase 1 Metabolism Reaction Library contains 159 reaction schemes based on cytochrome P450 (CYP450) phase one biotransformations. This reaction library was developed by ChemAxon. The reaction library is proprietary, so details of the reaction schemes cannot be viewed.
List of Schemes Included in ChemAxon's Human Phase 1 Metabolism Reaction Library (last updated July 2016)
PFAS Environmental Reaction Library
The PFAS Environmental Reaction Library has been developed to predict the likely environmental transformation products of per- and polyfluoroalkyl substances (PFAS). Version 1.1 of the PFAS Environmental Reaction Library contains 59 reaction schemes. The library is designed to run by itself and cannot be combined with other CTS reaction libraries. In the library documentation pages, left click a reaction scheme to view the generalized reaction scheme, example transformation pathways, and associated references. Scroll to the bottom of the library documentation page to view a table showing the rank assignments for each scheme in the library.
PFAS Environmental Reaction Library (last updated July 15, 2022)
PFAS Metabolic Reaction Library
The PFAS Metabolic Library has been developed to predict the likely transformation products of PFAS chemicals in biological systems. Version 1.1 of the PFAS Metabolic Reaction Library contains 76 reaction schemes. The library is designed to run by itself and cannot be combined with other CTS reaction libraries. In the library documentation pages, left click a reaction scheme to view the generalized reaction scheme, example transformation pathways, and associated references. Scroll to the bottom of the library documentation page to view a table showing the rank assignments for each scheme in the library.
PFAS Metabolic Reaction Library (last updated August 24, 2022)
Biotransformer Metabolism API
BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. Moreover, it can also assist scientists in the identification of metabolites, which is based on the metabolism prediction. BioTransformer uses both a knowledge-based approach and a machine learning based approach to predict small molecules metabolism. In particular, BioTransformer consists of five independent modules: EC-based, CYP450, Phase II, Human Gut Microbial and Environmental Microbial.
Visit biotransformer homepageExit
enviPath Pathway Prediction API
enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.