This repository contains chemical reactions data curation best practices.

• standardization protocol;
• a script to run the standardization protocol in parallel mode using chunks;
• a script for mappers comparison.

• Our golden dataset zip archive curated and mapped manually;
• USPTO dataset curated by the standardization protocol and mapped by RXNMapper.

Alexandre Varnek ([email protected])
Timur Madzhidov ([email protected])

Arkadii Lin ([email protected])
Ramil Nugmanov ([email protected])
Natalia Duybankova ([email protected])
Jonas Verhoeven ([email protected])
Timur Madzhidov ([email protected])
Alexandre Varnek ([email protected])
Joerg Wegner ([email protected])

Copyright 2020, MaDeSmart, Machine Design of Small Molecules by AI VLAIO project HBC.2018.2287

Kazan Federal University, Russia
University of Strasbourg, France
University of Linz, Austria
University of Leuven, Belgium
Janssen Pharmaceutica N.V., Beerse, Belgium
Rail Suleymanov, Arcadia, St. Petersburg, Russia

Please, cite the paper when you use the data or the scripts:

Lin, Arkadii; Dyubankova, Natalia; Madzhidov, Timur; Nugmanov, Ramil; Rakhimbekova, Assima; Ibragimova, Zarina; Akhmetshin, Tagir; Gimadiev, Timur; Suleymanov, Rail; Verhoeven, Jonas; Wegner, Jörg Kurt; Ceulemans, Hugo; Varnek, Alexandre (2020): Atom-to-Atom Mapping: A Benchmarking Study of Popular Mapping Algorithms and Consensus Strategies. ChemRxiv. Preprint. https://doi.org/10.26434/chemrxiv.13012679.v1

• python: 3.7
• CGRtools: 4.0.36
• ordered-set: 4.0.2
• pyjnius: 1.3.0
• JChemSuite package from ChemAxon: 19.9.0