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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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ChemBLAST: Old dog new tricks

31 Wednesday Dec 2014

Posted by chembioinfo in CDK, Java, Similarity

≈ 6 Comments

Tags

atoms, bitset, CDK, chemaxon, ChEMBL, circular fingerprints, EBI, EMBL, Similarity

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 homology searches (sequence similarity in large databases). Having said that, I would not like to discredit similar tools such as WU-BLAST, FASTA etc. I recently came across and read with great interest a wonderful paper from Baldi and Benz (3) highlighting the possibility of using this tool to fish out similar chemicals from databases. It touches upon a few statistical challenges and adaptations of Tanimoto scores for calculating the similarity of molecules. There are various ways for calculating chemical similarity i.e. graph based, fingerprint based etc. In today’s blog I will discuss using fingerprint based similarity methods to calculate similarity between molecules and how we can use this for BLASTing small molecules. The wiki has a rich page dedicate to the BLAST Tool.

Bringing Chemistry in the BLAST

  1. Calculate chemical fingerprints (binary: true, false) for a given molecule for size length L.
  2. Choose the indexes in the L which are set to true (for example, if bits 1, 10, 30,…. etc. are set as ‘true‘).
  3. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1->B$, 10->BA$, 30->DA$ …)
  4. Concatenate the patterns to form a sequence (B$BA$DA$…).
  5. While searching transform them as byte array and match them (treating the byte until $ as one letter).
  6. Create HSP tuple patterns and align the patterns using the BLAST algorithm.

Here it’s a basic/crude step towards an un-gapped alignment search which is fast yet powerful enough to bring out significant pattern matches between fingerprints sequence arrays.

Performance

In order to test the performances of the method I have chosen ChEMBL-19 dataset containing ~1.4 million molecules.

a) Preparing the ChEMBL-19 database for BLAST search by calculating HSP regions from fingerprints.

Note: This step is only required if a new database is released.

I have used ECFP4 (CDK CircularFingerprint).

Parallel implementation of BLAST search achieves 4X speed improvement, allowing gapped alignment for better coverage of hits.

 >sh format.sh data/chembl_19.txt
 Formatting input database....
 Running Time: 197.04 sec
 Index file created chembl_19.idx
 DB formatted chembl_19.fmt

b) Performing chemical similarity search on ChEMBL database.

I have chosen the query example selected by Andrew Dalke to test his chemfp-1.2 tool.

“CHEMBL23456″= CNC(=O)c1[nH]c2ccc(Cl)cc2c1Sc1ccccc1

sh search.sh data/chembl_19.txt "CNC(=O)c1[nH]c2ccc(Cl)cc2c1Sc1ccccc1"
Running Time: 70.36 sec, 11808 hits found.
Top 10 ChEMBL 19 hits reported by ChemBLAST tool for query molecule CHEMBL23456.

Top 10 ChEMBL-19 hits reported by ChemBLAST tool for query molecule CHEMBL23456.

The top 10 Hits from ChemBLAST tool:

Query Description:
> Query: CNC(=O)c1[nH]c2ccc(Cl)cc2c1Sc1ccccc1
Length = 158

	                 Bit    E-
Subject Description	 Score  Value
1>  CHEMBL23456         120  4e-26
2>  CHEMBL79468        79.7  4e-14
3>  CHEMBL82471        77.5  2e-13
4>  CHEMBL82052        72.5  7e-12
5>  CHEMBL286378       71.7  1e-11
6>  CHEMBL24273        69.6  5e-11
7>  CHEMBL445364       64.5  2e-09
8>  CHEMBL180330       63.7  3e-09
9>  CHEMBL286759       62.3  8e-09
10> CHEMBL2323896      62.3  8e-09
For example top two hits are aligned as:


> CHEMBL23456
Length = 158

Score = 120 bits (316), Expect = 4e-26
Identities = 158/158 (100%), Positives = 158/158 (100%), Gaps = 0/158 (0%)

Query     1  BK-KF-BDD-CBG-CCD-CHH-CIB-DHD-DHE-DIG-DKA-ECA-ECC-EEF-EGH-EI    60
             BK-KF-BDD-CBG-CCD-CHH-CIB-DHD-DHE-DIG-DKA-ECA-ECC-EEF-EGH-EI
Sbjct     1  BK-KF-BDD-CBG-CCD-CHH-CIB-DHD-DHE-DIG-DKA-ECA-ECC-EEF-EGH-EI    60

Query    61  G-FAF-FAH-FBE-FBF-FCB-FEK-FGK-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HE   120
             G-FAF-FAH-FBE-FBF-FCB-FEK-FGK-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HE
Sbjct    61  G-FAF-FAH-FBE-FBF-FCB-FEK-FGK-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HE   120

Query   121  G-HKG-IHA-IKI-KBE-KCG-KEH-KFA-KGH-KKH-   158
             G-HKG-IHA-IKI-KBE-KCG-KEH-KFA-KGH-KKH-
Sbjct   121  G-HKG-IHA-IKI-KBE-KCG-KEH-KFA-KGH-KKH-   158

> CHEMBL79468
Length = 154

Score = 79.7 bits (206), Expect = 4e-14
Identities = 129/149 (87%), Positives = 129/149 (87%), Gaps = 8/149 (5%)

Query     6  -BDD-CBG-CCD-CHH-CIB-DHD-DHE-DIG-DKA-ECA-ECC-EEF-EGH-EIG-FAF    65
             -B D-CBG-CCD-CHH-CIB-D  -DH -D  -DKA-E  -ECC-EEF-E  -EIG-FAF
Sbjct    10  -BHD-CBG-CCD-CHH-CIB-DGB-DHD-DHE-DKA-EAE-ECC-EEF-EIA-EIG-FAF    69

Query    66  -FAH-FBE-FBF-FCB-FEK-FGK-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HE----G   121
             -FAH-FBE-FBF-FCB-FE    K-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HE    G
Sbjct    70  -FAH-FBE-FBF-FCB-FE----K-FHG-GFD-GGB-HBC-HCG-HDH-HEA-HEG-HHG   125

Query   122  -HKG-IHA-IKI-KBE-KCG-KEH-KFA-   150
             -HKG-IHA-IKI-KBE-KCG-K H-K A-
Sbjct   126  -HKG-IHA-IKI-KBE-KCG-KGH-KHA-   154

Top 5 hits from Andrew Dalke‘s test case.

1 CHEMBL23456 1.00000
2 CHEMBL180330 0.94105
3 CHEMBL286759 0.93508
4 CHEMBL314618 0.93295
5 CHEMBL382002 0.92812

Thanks to John May, for providing the top 5 chemfp hits using the CDK ECFP4 (makes it an even playing ground as we both use the same fingerprints).

ChEMBL ID       Tanimoto Score
1 CHEMBL23456	1.00000
2 CHEMBL82471	0.77778
3 CHEMBL286378	0.74419
4 CHEMBL286759	0.71111
5 CHEMBL24273	0.70213

We all agree with the top hit CHEMBL23456, but we differ on the remaining top 4 hits. This could be due to the variation in choice of our fingerprints/methodology. Nonetheless, the top hits in both the cases looks interesting. I am sure there are many ways to reach the same goal and further optimisation of the code will make it even more attractive. Needs more playing around with!

Suggestions are welcome.

The ChemBLAST– tool is freely available on the GitHub for you to play with and its reasonably fast.

All things come to him who waits – provided he knows what he is waiting for. ~ Woodrow T. Wilson

—————————————————————————————————————————–

Basic principle of sequence BLAST

—————————————————————————————————————————–

To summarise a few of the important concepts:

a) It tries to compare gene sequences (amino acid or nucleotide) – query string against target string. BLAST will find conserved patterns in the database which are similar to sub-patterns in the query.

b) Its uses heuristics by calculating frequently occurring patterns called ‘high-scoring segment pair’ (HSP) in the database (using random walks). It then uses Gumbel extreme value distribution (EVD) to calculate the probability p of observing a score S equal to or greater than x. This is given by the equation:

In accordance with the Gumbel EVD, the probability p of observing a score S equal to or greater than x is given by the equation.

The statistical parameters \lambda and \mathrm{K} are estimated by fitting the distribution of the un-gapped local alignment scores of the query sequence and a lot of shuffled versions (global or local shuffling) of  database sequence patterns, to the Gumbel extreme value distribution.

c) W: Word/Pattern size – find W-mers (like n-grams) in target/query, T: Threshold – focus on pairs scoring >T, X: Drop-off – stop extending when loss > X, S: Score – the final score of segment pair.

Conditions: If W is too large, it will lead to too many patterns in L and vice versa – if too small, it will lead to too few patterns. If T is too large, then it’s very stringent (conserved blocks) and if too small, it will lead to too many extensions. Look for High-scoring Sequence Pairs (HSPs)-tuples and choose cut-off for relevant hits.

d) Find high scoring pattern of length W, and compile a list L of all W-mers that score >T with some pattern in query sequence. Then scan database for words in L and each positive hit is matched and extended. When score drops more than X below hitherto best score, stop extension. Now report all words with large score S.

References:

1) Altschul SF. et.al. Basic local alignment search tool: J Mol Biol. 1990 Oct 5;215(3):403-10. 

2) Altschul SF, et al. Gapped blast and psiblast: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. 

3) Baldi P. and Benz RW. BLASTing small molecules—statistics and extreme statistics of chemical similarity scores: Bioinformatics. Jul 1, 2008; 24(13): i357–i365.
52.205337 0.121817

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

11 Wednesday Apr 2012

Posted by chembioinfo in Enzymes, Java, Similarity, SMSD, Substructure, Work

≈ 5 Comments

Tags

Atom Atom Mapping, BioCyc, Bond Changes, BRENDA, chemaxon, ChEMBL, EBI, EC->PDB, EC-BLAST, EMBL, Enzyme Classification, Fingerprints, FunTree, health, Janet Thornton, KEGG, MACiE, medicine, Pathways, Reaction, Reaction Mechanism, Reaction Similarity, Rhea, science, Swissprot, technology, Toxicity, Uniprot

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, UniProt, EC->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.

http://www.ebi.ac.uk/thornton-srv/software/rbl/

http://www.ebi.ac.uk/thornton-srv/software/rbl/

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

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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 →
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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
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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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