BioTransformer 3.0

Added Abiotic transforamtion module (AbioticBio) including photochemical, chlorination and ozonation reactions.
Fixed a bug that the user can not download the results sdf or csv file when the substructure searching feature is not used

An improved BioTransformer 3.0 prediction program with a human reactant predictor

Added the feature that BioTransformer3.0 webserver will try to retrieve the predicted results from BTDB (BioTransformer Database in the webserver) to increase prediction speed.
- If the query molecule or any intermediate metabolite of the molecule was predicted by BioTransformer3.0 webserver before for the corresponding query biotransformer module and CYP450Mode parameter, the webserver will retrieve the results for it from BTDB.
- If the query molecule was not predicted before, the BioTransformer3.0 webserver will make full prediction for it and store the results into BTDB.
- If the molecule or any intermediate metabolite is an endogenous and matched in HMDB5.0, the results will still be retrieved from HMDB5.0.
Minor improvments and fixed bugs:
- The loading process of the result page and the filters methods are done on the server side now, so the user will be able to see the predicted results in time. This also solves the 504 time out error.
- Fixed a bug that when the query molecule contains some certain types of structures, a infinite loop bug will be triggered and the prediction will never finish.
- Change the daily limit restriction to 10 posts per minute.

Removed the Compound Identification module:
- The users can now use the filters provided on the result page to find the metabolites they want to identify, so we remove the Compound Identification module due to redundancy
Updated the prediction page:
- Optimized the layouts
- Added the parameter that allows the user to select the CYP450 metabolism prediction type, which are RuleBased;CyProduct;Combined
- Added more examples
Updated the results page:
- Added Chemical Formula and Result ID attributes
- Added SMILES String, Chemical Formula and min and max Mass filters to help the users find the metabolites of their interest quickly
- Optimized the format and fixed some wrong record issues in the downloaded .csv file

The GUIs and layouts of the BioTransformer 3.0 web server have been reimplemented Prediction page:
- Added the number of iterations feature on the prediction page, so the users can now select the number of iterations they want to apply for CYP450, ECBased, and allHuman metabolism modules
- Added the Custom Multi-Step Human metabolism module, so the users can now customize their own metabolic pathways by using different combinations of biotransformations
Result Page:
- The results page has been redesigned so the results are neat and clear to the users
BioTransformer 3.0 program improvements:
- Added machine-learned models for CYP450 metabolism module
- Added depolymerization functions to handle polymers
- fixing wrong SMIRKS reaction rules and adding new SMIRKS reaction rules in the knowledge-base
- connecting to HMDB5.0 to identify compounds and metabolites

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