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Evaluating the Quality and Performance of Automatic Atom Mapping Algorithms
- 1. Evaluating the Quality and Performance of Automatic Atom Mapping Algorithms Daniel Lowe and Roger Sayle NextMove Software Cambridge, UK ACS National Meeting, Philadelphia, USA 20th August 2012
- 2. What is Atom-Mapping? Mapping algorithm ACS National Meeting, Philadelphia, USA 20th August 2012
- 3. Why Perform Atom-Mapping? • Assigning roles to reagents • Normalization of reactions for registration ACS National Meeting, Philadelphia, USA 20th August 2012
- 4. Why Perform Atom-Mapping? • More precise database searches – Solvents/catalysts can be distinguished from reactants – Allows the relationship between the reactant atoms and product atoms to be made explicit ACS National Meeting, Philadelphia, USA 20th August 2012
- 5. Example • I want to find reactions converting an alkene to a cyclopropane so I search for C=C>>C1CC1 ACS National Meeting, Philadelphia, USA 20th August 2012
- 6. Why Perform Atom-Mapping? • Identifying suspect reactions: ACS National Meeting, Philadelphia, USA 20th August 2012
- 7. Qualities to look for in an atom mapping algorithm • Chemically plausible atom mappings • Ability to distinguish genuine reactants from solvents/catalysts • Support for unbalanced reactions – Side product not specified – Reactant stoichiometry > 1 • Fast run-time ACS National Meeting, Philadelphia, USA 20th August 2012
- 8. Algorithms Evaluated Vendor:Program Version ChemAxon:Marvin 5.10.1 GGA:Indigo 1.1 InfoChem:ICMAP 5.10 PerkinElmer:ChemDraw Ultra 12.0 ACS National Meeting, Philadelphia, USA 20th August 2012
- 9. Methodology Test set Reactions Pharmaceutical ELN subset 18,244 ChemReact68 database 67,926 SPRESI database subset 5,230 Reactions extracted from 2008- 562,872 2011 USPTO patent applications* * Lowe, D. M. Automated Extraction of Reactions from the Patent Literature. 243rd ACS National Meeting & Exposition, San Diego, CA, March 27, 2012. ACS National Meeting, Philadelphia, USA 20th August 2012
- 10. Methodology-cont. • Reaction SMILES were used as input and output for all algorithms bar ICMAP • Input and output was converted to and from RDF for use with ICMAP • Indigo was ran with its default configuration and more lenient settings for matching valences, charges and bond orders • Marvin was configured to use its best quality mapping strategy ACS National Meeting, Philadelphia, USA 20th August 2012
- 11. Ability to map all product atoms ACS National Meeting, Philadelphia, USA 20th August 2012
- 12. c-c bonds broken ACS National Meeting, Philadelphia, USA 20th August 2012
- 13. Speed Comparison Average 1.7 3.6 1.6 4.0 reagents per reaction ACS National Meeting, Philadelphia, USA 20th August 2012
- 14. Simple mappings Marvin/ChemDraw/Indigo/ICMAP ACS National Meeting, Philadelphia, USA 20th August 2012
- 15. Simple mappings Marvin/ChemDraw/Indigo/ICMAP ACS National Meeting, Philadelphia, USA 20th August 2012
- 16. More complicated Mappings Marvin ChemDraw ACS National Meeting, Philadelphia, USA 20th August 2012
- 17. More complicated Mappings Indigo ICMAP ACS National Meeting, Philadelphia, USA 20th August 2012
- 18. Reuse of reactants ACS National Meeting, Philadelphia, USA 20th August 2012
- 19. Reuse of reactants Marvin ACS National Meeting, Philadelphia, USA 20th August 2012
- 20. Reuse of reactants ChemDraw ACS National Meeting, Philadelphia, USA 20th August 2012
- 21. Reuse of reactants Indigo ACS National Meeting, Philadelphia, USA 20th August 2012
- 22. Reuse of reactants ICMAP ACS National Meeting, Philadelphia, USA 20th August 2012
- 23. Single Atom Mapping ICMAP/Marvin ChemDraw/Indigo ACS National Meeting, Philadelphia, USA 20th August 2012
- 24. Bugs and quirks • Marvin – 2 unsuccessful mappings produced unchecked exceptions rather than checked exceptions • ChemDraw – Hydrogen on aromatic atoms missing in SMILES output • Indigo – Calculation of valency fails for aromatic sulfur ACS National Meeting, Philadelphia, USA 20th August 2012
- 25. Bugs and quirks • ICMAP – Single atom products are interpreted as empty molecules or occasionally replaced by a product from a previous reaction (bug reported) – Input files must be < 2gb and use dos line endings ACS National Meeting, Philadelphia, USA 20th August 2012
- 26. conclusions • ICMAP produced the best quality mappings on the tested sets • Atom mapping isn’t as simple as finding a maximum common subgraph mapping • In all the algorithms there were aspects that could be improved to yield appreciable benefits ACS National Meeting, Philadelphia, USA 20th August 2012
- 27. acknowledgements • Ed Griffen and Nick Tomkinson, AstraZeneca. • Andrew Wooster, GSK. • Hans Kraut, InfoChem • Thank you for your time. ACS National Meeting, Philadelphia, USA 20th August 2012