Protein-Protein Interactions

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Protein-Protein Interactions
Simon Kanaan Computer Science and
Engineering University of Notre Dame
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Why Bother Studying Protein-Protein (p-p)
Interactions?

• Protein-Protein interactions occur in any living
  organism.
• Scientists can not test all the combinations of
  Proteins since there are too many proteins, and
  they are not easy to isolate
• Knowledge of p-p interactions allows us to
  understand the internal structures of a living
  organism.

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Background

• Biological Research has given us some knowledge
  of the structure of proteins.
• Proteins contain a sequence of information called
  a domain, where each protein contains a certain
  number of domains.
• There are large databases containing p-p
  interactions and their domains, which are derived
  from enormous amounts of lab experimentation

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How Do We Plan on Predicting p-p interactions?

• We are able to predict which proteins interact
  with which by looking at the domain level.
• We have written a number of algorithms all of
  which look at the p-p pairs known and attempt to
  figure out which pair of domains explains each of
  the interactions.

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Implemented Algorithms

• ChengBang's algorithm
• -constructs a vector of most common interacting
  domain-domain (D-D) pair to least common needed
  to explain all P-P interactions given in input
  file.
• Simon's algorithm
• -constructs a vector starting from most common
  interacting D-D pair of the most common domain
  needed to explain all P-P interactions given in
  input file.

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Algorithms in Progress
Chengbang's and Simon's algorithms with the
following modifications -taking into
consideration absence of edges by subtracting by
one in our D-D matrix for every missing
edge. -instead of only taking into account the
most common D-D interaction of the most frequent
domain, take all D-D interactions from most to
least common of most frequent Domain.
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Direction We Are Heading

• Our first step is to finish implementing all the
  algorithms explained in this presentation
• Second, there are a a couple more complicated
  algorithms being looked at/developed which will
  also need to be implemented.
• We also need to test our algorithms to see how
  robust and accurate they are.