Important Notice

BioTransformer’s environmental microbial degradation module uses data from the EAWAG’s Biodegradation and Biocatalysis Database, which is licensed by EnviPath under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International. Therefore users of the environmental microbial degradation module must cite the EnviPath paper below (See Cite section). To use the environmental microbial module for commercial purposes, users must request an appropriate commercial license from EnviPath.

BioTransformer’s README

This is version 3.0.0 of BioTransformer. BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, based on the metabolism prediction. Please make sure to download the folders database and supportfiles, and save them in the same folder as the .jar file.

BioTransformer is offered to the public as a freely accessible software package under the GNU LGPL, version 3 license. Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and build upon the material under the condition that they must give appropriate credit, provide links to the license, and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to acknowledge the authors.

Cite:

Djoumbou Feunang Y, Fiamoncini J, de la Fuente AG, Manach C, Greiner R, and Wishart DS; BioTransformer: A Comprehensive Computational Tool for Small Molecule Metabolism Prediction and Metabolite Identification; Journal of Cheminformatics; (2019) 11:2; DOI: 10.1186/s13321‐018‐0324‐5.

Contact

To report issues, provide feedback, or ask questions, please send ane-mail the following address: djoumbou@ualberta.ca

Usage: java -jar biotransformer-3.0.0.jar -k -b [-ismi, -imol, or -isdf ] [-imol, or -isdf ] [-s ] [-a ] [-m ] [-r ] [-f ] [-q ] [-cm ]

This is the version 3.0.0 of BioTransformer. BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut microbiota, as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification, based on the metabolism prediction.

-a,–annotate Search PuChem for each product, and annotate with CID and synonyms

-b,–btType The type of description: Type of biotransformer - EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut microbial (hgut), human super transformer** (superbio, or allHuman), Environmental microbial (envimicro)*.

-cm, cyp450mode CYP450 prediction Mode here: 1) CypReact + BioTransformer rules; 2) CyProduct only; 3) Combined: CypReact + BioTransformer rules + CyProducts. Default mode is 1.

-h,–help Prints the usage.

-ismi, –ismiles < Input > Read the input as a single molecule in SMILES format

-imol, –molinput Read the input as a single molecule in the specified MOL format

-isdf, –sdfinput Read the input from the specified SDF format

-k, –task The task to be permed: pred for prediction, or cid for compound identification

-m,–mList Given the starting compound(s), Find all their metabolites with the specified masses, and show a metabolism pathway. A whitespace-separated list of masses is expected.

-ocsv, –csvoutput Save the results into the specified CSV file

-osdf, –sdfoutput Save the results into the specified SDF file

-f,–formulas Semicolon-separated list of formulas of compounds to identify
-s,–nsteps The number of steps for the prediction. This option can be set by the user for the EC-based, CYP450, Phase II, and Environmental microbial biotransformers. The default value is 1.

-q, –bsequence Ordered Sequence of biotransformation steps. Semi-colon separated pairs of biotransformer types and corresponding number of steps to be simulated.

-t,–mTolerance Mass tolerance for metabolite identification (default is 0.01).

(* ) While the ‘superbio’ option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation first, then Oxidation/reduction, etc.), the ‘allHuman’ option predicts all possible metabolites from any applicable reaction(Oxidation, reduction, (de-)conjugation) at each step.

(** ) For the environmental microbial biodegradation, all reactions (aerobic and anaerobic) are reported, and not only the aerobic biotransformations (as per default in the EAWAG BBD/PPS system).

Examples:

To predict the biotransformation of a molecule from an SDF input using the human super transformer (option superbio) and annotate the metabolites with names and database IDs (from PubChem), run

java -jar biotransformer-3.0.0.jar -k pred -b superbio -isdf -i #{input file name} -osdf #{output file} -a.
To predict the 2-step biotransformation of Thymol (a monoterpene) using the human super transformer (option allHuman) using the SMILES input, cypMode = 3 (combined mode), and saving to a CSV file, run

java -jar biotransformer-3.0.0.jar -k pred -b allHuman -ismi “CC(C)C1=CC=C(C)C=C1O” -ocsv #{replace with output file name} -s 2 -cm 3

Currently, the outputfile is SDF per default.

Identify all human metabolites (max depth = 2) of Epicatechin (“O[C@@H]1CC2=C(O)C=C(O)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1”) with masses 292.0946 Da and 304.0946 Da, with a mass tolerance of 0.01 Da. Provide an annotation (Common name, synonyms, and PubChem CID), when available.

java -jar biotransformer-3.0.0.jar -k cid -b allHuman -ismi “O[C@@H]1CC2=C(O)C=C(O)C=C2O[C@@H]1C1=CC=C(O)C(O)=C1” -osdf #{replace with output file name} -s 2 -m “292.0946;304.0946” -t 0.01 -a
- DO NOT forget the quotes around the SMILES string or the list of masses.
Simulate an order sequence of metabolism of Atrazine (“CCNC1=NC(=NC(=N1)Cl)NC(C)C”), starting with two steps of Cyp450 oxidation, followed by one step of conjugation.

java -jar biotransformer-3.0.0.jar -ismi “CCNC1=NC(=NC(=N1)Cl)NC(C)C” -osdf ~/atrazine-sequence.sdf -k pred -q “cyp450:2; phaseII:1” To report issues, provide feedback, or ask questions, please send an e-mail the following address: djoumbou@ualberta.ca

Compiling and packaging BioTransformer with Maven:

To compile BioTransformer and package it into an executable .jar file, you need to have maven (v >3.6) installed. Then run:

1. cd biotransformer
2. ./install-via-maven.sh