Asad's Blog

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Tag: Reaction

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 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).

EC-BLAST Tutorial for Hands-on Training

EC-BLAST Tutorial for Hands-on Training

Publication: 

EC-BLAST: a tool to automatically search and compare enzyme reactionsSA Rahman, SM Cuesta, N Furnham, GL Holliday, JM Thornton; Nature methods 11 (2), 171-174

EC-BLAST: A Novel Tool for Finding Chemically Similar Enzymes

Enzymes have been part of our evolutionary machinery and it’s importance is ever increasing in our life. An enzymatic hierarchal functional classification has been developed to cluster similar enzymes based on its chemistry (kindly refer to my previous blog on enzymes). A parallel system envolves sequence and protein structural based classification systems. One of the most challenging issues in todays bio/chemo informatics science is to automatically link the sequence knowledge with the enzymatic chemistry. There exists many methods in the literature addressing this issue but its hard to find a direct link which can hold true for all the cases. Although, very recently in the Prof. Janet Thornton’s group we have come up with a web tool – “FunTree” for linking enzyme super families based on the knowledge of the evolution, derived from sequences and structures (proteins and small molecules). It’s very enigmatic to find a one to one mapping between genes->protein->enzymes and its equally mind boggling to navigate in this space. This is one of the reasons why we have many orphan enzymes or enzyme which do not have a sequence assigned to it yet. On one hand we have ever increasing sequence database and sophisticated tools like BLAST and FASTA to compare them. Unfortunately, the bio-chemical side of the story is slow as we have limited number of publicly available chemical databases and tools in chemistry. Although in the recent years there has been databases like BRENDA, KEGG, BioCyc, UniProtEC->PDB and SwissProt etc. to bring forth and link sequence to chemistry. There are efforts to link up various resources of enzyme chemistry under an umbrella and one such web portal is “Enzyme Portal“. Likewise there exists, few curated databases linking enzyme function and reaction mechanism like MACiE , Rhea and SFLD etc.

The challenge for a biologist/chemist is find a tool which can function like BLAST (as a magic black box) in finding similar enzymes in a reaction database (needle in a haystack). The good new is that we have made some progress in this interesting area of research by coming up with a novel tool – “EC-BLAST“. The core idea behind this tool is to find similar enzymes ranked by similarity of the bond changes, reaction center or chemical structural similarity of the participating reactions. One could start a search with a molecule/reaction name or its structure. The Atom-Atom Mapping (AAM) is algorithmically generated on the fly for a balanced input reaction and the bond changes are automatically deduced and marked before performing any search.

EC_BLAST Front Page

EC BLAST front page

The cognisance of search results would channelise us to gain better insight into the catalytic promiscuity of the enzymes and complement the sequence based results obtained from tools like BLAST, FASTA etc (where the chemistry in not necessarily retained in the results). This will help us to link up the evolutionary and mechanistic aspects of the enzymes, in the biological findings with chemical knowledge.

Such tools will also help us gain better insight into toxicity studies (can be a value added parmeter to the likes of ChEMBL/DrugBank), in designing novel enzyme and retrosynthetic pathways etc. Although the first glimpse of the EC-BLAST was unveiled at the ISMB 2011, Vienna where it won the “Killer Apps 2011″ award, it largely remained restricted to the EBI and collaborators. The response at the ISMB 2011 (poster here) was very encouraging for us and there has been an ever increasing need, scope and requisition for such a resource. Hence, we have now decided to go public with a beta version of our web portal service.
EC-Blast result page for bond change similarity searches.

EC-Blast result page for bond change similarity searches.

Note: If you are interested in testing this service or sending us your comments or feedbacks, please do let me know!

Publication: Rahman, S.A., Martinez Cuesta, S., Furnham, N., Holliday, G.L. and Thornton, J.M. (2014) EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions. Nat Methods, DOI: 10.1038/nmeth.2803

How are enzymes classified?

How are enzymes classified?

Metabolism influences building or replacement of tissue, conversion of food to energy, disposal of waste materials, reproduction etc. “Catalysis” is defined as the acceleration of a chemical reaction by a substance which itself undergoes no permanent chemical change. Most biochemical reactions do not take place spontaneously and enzyme catalysis plays an important role in biochemical reactions necessary for all life processes. Without enzymes, these reactions would take place at a rate far too slow for effective metabolism.

Enzymes can be classified by the kind of chemical reaction they catalyze. One such scheme of enzyme classification is defined by IUBMB.

The IUBMB assigns a 4-digit code to each enzyme. Each enzyme is prefixed by EC, followed by the digits.

For exampleoxidoreductases EC 1.1.1.1

1.     The first digit denotes “Class” of the enzyme

2.     The second digit indicates, “Sub-class” of the enzyme

3.     The third digit gives “Sub sub-class” of the enzyme

4.     The fourth digit in the code is “Serial number” of the enzyme

The classification is as follows:

Group Name Type of Reaction Catalysed Example
Oxidoreductases Oxidation-reduction reactions Alcohol oxidoreductase (EC 1.1)
Transferases Transfer of functional groups Methyltransferase (EC 2.1)
Hydrolases Hydrolysis reactions Lipase (EC 3.1)
Lyases Addition to double bonds or single bonds Decarboxylases (EC 4.1)
Isomerases Isomerization reactions Epimerases and Racemases (EC 5.1)
Ligases Formation of bonds with ATP cleavage Enzymes forming carbon-oxygen bonds (EC 6.1)

b) How can I find similar enzymes?

Any similarity search is based on the presence of similar patterns (similar bond changes and/or small molecules) shared between query and target reactions. A large number of shared patterns results in higher similarity score or lesser distance score. In Bioinformatics, the concept of similarity or distance is used to find similar sequences based on amino acid similarity, structural topology, etc. In Chemoinformatics similarity between small molecules/drug molecules (i.e. based on Tanimoto score) is based on the presence of similar bonds and atoms between query and target molecules.

c) Literature

  1. Automatic Assignment of EC Numbers.
  2. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
  3. Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database.
  4. Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps.
  5. Chemical similarity searching.
  6. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  7. Using Reaction Mechanism to Measure Enzyme Similarity
  8. etc.

I reckon in the near future we might see such concepts being adapted by IUBMB itself to annotate and classify enzymes.

This would be vital in the study of the interactions between the components of biological systems (metabolites, enzymes and metabolic pathways), and how these interactions give rise to the function and behavior of that system.

As always, thoughts/suggestions are welcome!

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