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Tag Archives: SMILES

Atom Atom Mapping (AAM) and Challenges

18 Tuesday Mar 2014

Posted by chembioinfo in Atom Typing, CDK, EC-BLAST, Enzymes, Java, Similarity, SMSD, Substructure, Work

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Tags

AAM, Atom Atom Mapping, Atom Mapping, CDK, EC-BLAST, Enzymes, Reaction, Rhea, RXN, SMILES, SMSD

We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from Github. 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.

Atom Atom Mapping (AAM) Tool can be downloaded via SF – https://github.com/asad/ReactionDecoder

The key features of this tools are:

  • Maps reactions catalysed by enzymes.
  • 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: 10/Nov/2016

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]

Few test case can be found here https://github.com/asad/AAMTool.

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

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RSS Asad’s Blog

  • A Romance between Biology and Chemistry – Protein Sequences, Molecules and Enzyme function! August 15, 2015
    Next Generation Sequencing (NGS) data is knocking at our door and simultaneously, our ability to design novel enzymes (rational design or directed …Continue reading →
    chembioinfo
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    chembioinfo
  • Atom Atom Mapping (AAM) and Challenges March 18, 2014
    We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from …Continue reading →
    chembioinfo
  • EC-BLAST Tutorial for Hands-on Training February 4, 2014
    EC-BLAST Tutorial for Hands-on Training Publication:  EC-BLAST: a tool to automatically search and compare enzyme reactions, SA Rahman, SM Cuesta, N …Continue reading →
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  • Shortest Path and Molecular Hashed Fingerprints July 23, 2012
    Shortest Path (SP) has been used in many aspects of graph traversing. The idea is to minimise the cost (number …Continue reading →
    chembioinfo
  • EC-BLAST: A Novel Tool for Finding Chemically Similar Enzymes April 11, 2012
    Enzymes have been part of our evolutionary machinery and it’s importance is ever increasing in our life. An enzymatic hierarchal …Continue reading →
    chembioinfo
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    Edited: 4th Nov, 10:20 AM In my previous post, I discussed the impact of the hashcode and random number generators …Continue reading →
    chembioinfo
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    Ingredients: 3 tsp. of Tea Leaves (you can use the Indian tea bags if preferred…Assam/Darjeeling etc) ½” piece of Ginger crushed …Continue reading →
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I Voted

Top Posts & Pages

  • How are enzymes classified?
  • Ultra Fast substructure search based on the VF2 outperforms CDK UIT
  • EC-BLAST: A Novel Tool for Finding Chemically Similar Enzymes
Follow Asad's Blog on WordPress.com

Enter your email address to follow this blog and receive notifications of new posts by email.

Recent

  • A Romance between Biology and Chemistry – Protein Sequences, Molecules and Enzyme function! August 15, 2015
  • ChemBLAST: Old dog new tricks December 31, 2014
  • Atom Atom Mapping (AAM) and Challenges March 18, 2014
  • EC-BLAST Tutorial for Hands-on Training February 4, 2014
  • Shortest Path and Molecular Hashed Fingerprints July 23, 2012

Archives

Tags

Atom typing bitset BRENDA CDK chemaxon circular fingerprints EBI EC Number Enzyme Classification Fingerprints hashCode() hashed fingerprints Indian Isomorphism IUBMB enzyme nomenclature Java join Structures KEGG MACiE MCS Mersenne Twister Random() Reaction Reaction Similarity Similarity Small Molecule SMSD substructure Tanimoto VF2

Blogroll

  • Andrew Dalke
  • ChEMBL
  • Christoph Steinbeck
  • Egon Willighagen
  • Gilleain Torrance
  • Joerg Kurt Wegner
  • Niyaz Ahmed
  • Noel O'Blog
  • Rajarshi Guha
  • Richard Apodaca

RSS Asad’s Blog

  • A Romance between Biology and Chemistry – Protein Sequences, Molecules and Enzyme function! August 15, 2015
    Next Generation Sequencing (NGS) data is knocking at our door and simultaneously, our ability to design novel enzymes (rational design or directed …Continue reading →
    chembioinfo
  • ChemBLAST: Old dog new tricks December 31, 2014
    Updated:07/01/2015 BLAST-Basic Local Alignment Tool was born in the 1990s (1,2) and has since been the bread and butter of …Continue reading →
    chembioinfo
  • Atom Atom Mapping (AAM) and Challenges March 18, 2014
    We have just released our long awaited AAM tool in the public domain…this was long over due! You can download the tool from …Continue reading →
    chembioinfo
  • EC-BLAST Tutorial for Hands-on Training February 4, 2014
    EC-BLAST Tutorial for Hands-on Training Publication:  EC-BLAST: a tool to automatically search and compare enzyme reactions, SA Rahman, SM Cuesta, N …Continue reading →
    chembioinfo
  • Shortest Path and Molecular Hashed Fingerprints July 23, 2012
    Shortest Path (SP) has been used in many aspects of graph traversing. The idea is to minimise the cost (number …Continue reading →
    chembioinfo
  • EC-BLAST: A Novel Tool for Finding Chemically Similar Enzymes April 11, 2012
    Enzymes have been part of our evolutionary machinery and it’s importance is ever increasing in our life. An enzymatic hierarchal …Continue reading →
    chembioinfo
  • Improved CDK Hashed Fingerprinter November 4, 2011
    Edited: 4th Nov, 10:20 AM In my previous post, I discussed the impact of the hashcode and random number generators …Continue reading →
    chembioinfo
  • Revisiting Molecular Hashed Fingerprints October 30, 2011
    Introduction Fingerprints have been widely used in various fields to find similar features. Now for those of you who are …Continue reading →
    chembioinfo
  • Thread safe SMSD September 14, 2011
    How can I run SMSD using Java Thread….is SMSD thread safe? The short answer is “YES” you can. Here is …Continue reading →
    chembioinfo
  • Indian Style Ginger Tea August 20, 2011
    Ingredients: 3 tsp. of Tea Leaves (you can use the Indian tea bags if preferred…Assam/Darjeeling etc) ½” piece of Ginger crushed …Continue reading →
    chembioinfo
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