Atom Atom Mapping (AAM) and Challenges

We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from sourceforge. This tool is based on the algorithm published in the SA Rahman et.al. (2014) Nature Methods paper. We have successfully mapped more than 6000 KEGG reactions in the EC-BLAST.

The key features of this tools are:

  • Maps reactions catalysed by enzymes.
  • Reactions have to be chemically balanced (at least non hydrogen atoms, i.e. Carbon, Nitrogen etc.). Semantically speaking, total number of atoms on the left hand = total number of atoms on the right hand.
  • Generates images of the mapped reactions where matching substructures are highlighted.
  • Generates reaction patterns and bond changes for input reactions.
  • The input format can be SMILES or RXN file.
  • This is build on the SMSD and CDK, hence its pure Java (7.0), thus platform independent.

Updated: 12/Dec/2014

For example KEGG reaction R03621 coded by EC 2.3.1.2 is:

a) Mapped reaction images as png.

Atom Atom Mapping by EC-BLAST

Atom Atom Mapping by EC-BLAST

 

b) Reaction AAM details, Bond changes and Reaction Patterns in this file.

I have a list of challenging cases which we have logged, which I think may be interesting to put in the public domain.

For example:

Case 1: 

case1

Expected Mapping: 

[O:10]=[C:9]([OH:11])[CH2:8][CH:6]([O:5][C:3](=[O:4])[CH2:2][CH:12]([OH:14])[CH3:13])[CH3:7].[H:16][OH:1]>>[H:16][O:5][CH:6]([CH3:7])[CH2:8][C:9](=[O:10])[OH:11].[O:4]=[C:3]([OH:1])[CH2:2][CH:12]([OH:14])[CH3:13]

Case 2: 

case2

Expected Mapping:

[O:10]=[C:8]([OH:7])[C:11]([O:12][CH:13]1[CH:9]=[CH:5][CH:14]=[C:15]([C:6](=[O:4])[OH:3])[CH:16]1[OH:2])=[CH2:1]>>[O:10]=[C:8]([OH:7])[C:11]([O:12][CH:13]1[CH:16]=[C:15]([CH:14]=[CH:5][CH:9]1[OH:2])[C:6](=[O:4])[OH:3])=[CH2:1]

I would like to hear from the developers and users….Challenges and Use cases!

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