Atom Atom Mapping (AAM) and Challenges

by chembioinfo

We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from SF and it’s README file. This tool is based on the algorithm published in our recent 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: 21/March/2014

As a test case we have mapped more than 4000 Rhea reactions and the results are available here.

For example Rhea reaction 15814 coded by EC 2.3.1.2 is:

a) Mapped reaction images as png.

b) Mapped reaction RXN file.

c) Reaction AAM details, Bond changes and Reaction Patterns as XML 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]

Case 3:

case3

Expected Mapping:

[H:45][C:13]([NH2:27])([C:14](=[O:15])[OH:16])[CH2:17][c:18]1[cH:19][nH:20][c:21]2[cH:26][cH:25][cH:24][cH:23][c:22]21.[O:3]=[C:2]([OH:4])[C:1](=[O:12])[CH2:5][c:6]1[cH:7][cH:8][cH:9][cH:11][cH:10]1>>[O:15]=[C:14]([OH:16])[C:13](=[O:12])[CH2:17][c:18]1[cH:19][nH:20][c:21]2[cH:26][cH:25][cH:24][cH:23][c:22]21.[H:45][C:1]([NH2:27])([C:2](=[O:3])[OH:4])[CH2:5][c:6]1[cH:7][cH:8][cH:9][cH:11][cH:10]1

Case 4:

case4

Expected Mapping:

[H:23][C:1]([NH2:9])([C:2](=[O:3])[OH:4])[CH2:5][CH2:6][S:7][CH3:8].[O:14]=[CH:10][C:11](=[O:12])[OH:13]>>[O:3]=[C:2]([OH:4])[C:1](=[O:14])[CH2:5][CH2:6][S:7][CH3:8].[H:23][CH:10]([NH2:9])[C:11](=[O:12])[OH:13]

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

 

PS: Blog reaction images were rendered using Chemaxon (Marvin).