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Tag Archives: EC Number

A Romance between Biology and Chemistry – Protein Sequences, Molecules and Enzyme function!

15 Saturday Aug 2015

Posted by chembioinfo in Work

≈ 3 Comments

Tags

AAM, Biomarker, Bond Changes, Classification, Directed evolution, EBI, EC Number, EMBL-EBI, Enzyme Classification, Functional genomics, Genes, Github, GO, KEGG, Metabolic pathways, Metabolomics, MMP, Novel Genes, Nutrigenomics, Ontology, Predicting, Protein Sequence, Rational design, Reaction Similarity, Seq2EC, Sequence, Small Molecule, substructure, Toxicity

Next Generation Sequencing (NGS) data is knocking at our door and simultaneously, our ability to design novel enzymes (rational design or directed evolution) using high throughput methods has improved tremendously. As a result, the demand to link enzymatic sequences to their chemical products and metabolic pathways is ever increasing.  On the other hand, the push to generate Metabolomics data to design Biomarkers, understand Toxicity, Functional genomics and Nutrigenomics has given researchers a run for their money!

Last year we launched EC-Blast (my old post), a robust tool to compare chemical reactions using chemical knowledge of bond changes, molecule molecule pair (MMP) and molecule substructures. This tool helps plough through and understand the reactions present in the Enzyme Commission (E.C.) classification. This has generated a lot of interest in the research community and industry to revisit and mine the knowledge which might have been overlooked by traditional methods. Feedbacks from our users strongly suggested a demand for tools/methods to systematically link the protein sequences to the knowledge of bond changes, molecule molecule pair (MMP) and molecules substructures.

We have recently developed Sequence to Enzyme (Seq2EC) a novel tool (Figure 1) to:

  • Detect novel enzymatic genes- test if a sequence has potential enzymatic function.
  • Predict GO terms, E.C. number, bond changes and MMP from a protein sequence.
  • Predict potential genes and protein domains from chemical bonds (e.g. O-C, O-P formed or cleaved).
Seq2EC: A robust tool to predict/detect enzyme from protein sequence

Figure 1: Predicting enzyme function from protein sequence

There are two ways to use the tool:

  1. Seq2EC webservice/webserver (requires patience): http://www.ebi.ac.uk/thornton-srv/software/rblec/
  2. Download and run locally (fast) – contact me!

The tool reports a star ranking schema (Table 1) for predicted enzymes which is based on the statistical confidence of finding domains, bonds, catalytic sites etc.

Table 1: Star ranking schema explained

Star Rank Note
**** Platinum Confident till the 4th level of EC
*** Gold Confident till the 3rd level of EC
** Silver Confident till the 2nd level of EC
* Bonze Confident till the 1st level of EC
. Ambiguous Might have an enzymatic activity

Please go ahead and test your favourite sequence(s) or chemical changes and send me your feedback/comments!

52.205337 0.121817

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EC-BLAST Tutorial for Hands-on Training

04 Tuesday Feb 2014

Posted by chembioinfo in EC-BLAST, Enzymes, Java, Work

≈ 2 Comments

Tags

CDK, EC Number, Enzyme Classification, Fingerprints, Isomorphism, IUBMB enzyme nomenclature, Java, KEGG, MACiE, MCS, Reaction, Similarity, Small Molecule, SMSD

EC-BLAST Tutorial for Hands-on Training

Publication: 

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

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How are enzymes classified?

03 Thursday Mar 2011

Posted by chembioinfo in Enzymes, Similarity, Work

≈ 8 Comments

Tags

BRENDA, EC Number, Enzyme, Enzyme Classification, IUBMB, IUBMB enzyme nomenclature, KEGG, MACiE, Reaction, Small Molecule, Tanimoto

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 example: oxidoreductases 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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  • 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

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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

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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
  • 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
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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