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SAR_EMBL_EBI_EC_BLAST_NOV_2013_Industry_workshop
1. EC-BLAST: A Novel Tool for
Finding Chemically Similar
Reactions
Dr. Syed Asad Rahman
asad@ebi.ac.uk
Thornton Group
Computational Tools for Chemical Biology
Nov-2013
3. How to classify and compare enzymes?
• Find similar enzymes which can perform similar task
(Superfamily)
• Design de-novo enzymes and small molecule pathway
analysis
• Optimise enzymes of commercial importance
• Drug and mode of action/ cross reactivity
• Assignment/Clustering of EC numbers based on the
quantitative measure
5. ECBLAST
S. A. Rahman et. al.,
EC-BLAST: A Tool to Automatically
Search and Compare Enzyme
Reactions, Nature Methods
(accepted)
http://www.ebi.ac.uk/thornton-srv/software/rbl/
10. Linking Sequence Domains and Chemical
Attributes
• Find all the sequence domains using Pfam/CATH
• Find all the chemical attributes interacting with those
domains from EC-BLAST DB
• Report the chemical features and common substructure
Chemical Domains Sequence
EC: 6.2.1.* Pfam: PF00501-AMP-binding UniProt:
Q6FLU2
Core
Fragment
11. Future
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Integrated database with Rhea and BRENDA reactions
~ 15,000 Reactions linked to UniProt, Pfam etc
Link Chemistry to Sequence
Toxicity
Web service
Collaborations
12. Acknowledgements
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Gemma L. Holliday
Gilleain Torrence
Franz Fenninger
Lorenzo Baldacci
Dame Prof. Janet M. Thornton
Nicholas Furnham
Sergio Martinez Cuesta
• Nimish Gopal, Sophie Williams and Saket Choudhary
• Funded by
14. Warm up exercise
• Reaction similarity search using EC 6.1.1.1
• Look at the similarity scores and the top 10 hits.
• EC number and linked information (Pfam, PDB etc) by
clicking on them
15. Exercise 1
• Search for “penicillin G” using molecule search option in
the EC-BLAST