Predicting Molecular Changes Catalyzed by Enzymes

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Predicting Molecular Changes Catalyzed by Enzymes

• MSCS 228
• Dr. Struble
• Group Gowri, Jack, Minesh

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Introduction
Molecular change in this example is -C-O-H
-C-H Enzyme MIEDIKTLRE EHVYRAKLAE
QAERYDEMAE AMKNLVENCL
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Enzymes in a Multiple Sequence Alignment
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Task

• Build a classifier using enzyme sequences that
  predicts molecular change
• For ex. For molecular change O-H -OPO4,
  lets say the enzymes involved are e1, e2, e3,
  en
• Given a new enzyme sequence we should be able to
  predict if it can catalyze reactions involving
  the change O-H -OPO4

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Methods
KEGG Reactions
Molecular Changes (?mc ) Graph Isomorphism
Multiple Sequence Alignment for each functional
class ClustalW MEME
Get ECs involved in each ?mc or each Molecular
class
Build Hidden Markov Model HMM Build
Get amino acid Sequence For each functional
class BRENDA
Predict Functional Class for novel
sequences HMMAlign, HMM Pfam
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HMMs

• HMMBuild Makes a statistical model of family of
  enzymes using MSA
• HMMsearch Uses model to assign a probability
  that a new sequence is a member of the family.

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Results
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Future Directions

• Improve upon sequence selection for building the
  HMMs to identify all sequences for a molecular
  change
• Use HMMs find conserved domains for a given
  molecular change and then mine that data for
  prediction