AutomN

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AutomN

• An Automated Protein Sequence to iNteraction
  Generator

Nick Lyle, Kanwal Brar, Inna Williams
Advisors Brian Beck, Sergiu Dascalu
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Overview

• What does AutomN do?
• General Biochemistry Concepts
• AutomN Applications
• What is it for?
• How is it different?
• Technical Details
• Requirements
• Data Flow
• GUI Philosophy and Example
• Future Work

Brar
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AutomN

• Takes 2 protein sequences, outputs docked protein
  structures of these proteins
• Data pipeline with many modules
• Helps determine protein interaction networks -
  Drug Design
• Ties together complicated steps in automated
  mater

Nick
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Proteins What are they?

• Proteins (Enzymes) run chemical reactions
• Substrate ? Product
• Usually 1 unique protein for EVERY unique
  reaction

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Protein-Protein Docking

• Some proteins dock (stick) to each other in a
  highly specific way
• The final complex is functional
• Individual pieces are not
• Some docking
• modifies protein
• behavior

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What are proteins?

• Regular protein 100-400 AAs

Sequence Ordered list of all amino acids (20
possible) in a protein from the amino-terminal
end to the carboxyl-terminal end. This sequence
determines the protein structure. LSTQSALSKDPNEKRD
HMVL
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AutomN Applications

• Research tool
• Map organism
• Drug development
• Helps predict protein complexes and interactions
• Pieces of this process defined
• AutomN ties it all together (the difference)
• Transforms input from one prog. to another
• Just a guess!
• Eliminate many options
• Leave only a few to test

Inna
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So Many Reactions!
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Main Requirements

• The AutomN system shall take two protein
  sequences as input, preferably in FASTA format.
• The AutomN system shall acquire one protein
  structure file in PDB format for each protein
  sequence if the protein structure file exists.
• The AutomN system shall generate a protein
  structure prediction in PDB format for each
  protein sequence if a pre existing PDB file can
  not be found.
• The AutomN system shall dock the two PDB files
  derived from the input protein sequences.
• The AutomN system shall present to the user in
  graphical format all possible docked structures
  so the user can manually choose the best docked
  structure if desired.
• The AutomN system shall compile on all platforms
  that support the software modules that AutomN
  uses.
• The AutomN system shall make the process as
  automated as possible by minimizing the user
  interaction required to use AutomN.

Brar
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Data Flow

• Note Extensible
• can use any other
• software modules

Inna
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GUI Example

• Collect all input, then run uninterrupted

Nick
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Final Output

• Possible
• docked
• structures
• -User selects
• best
• Structures
• -Ranked based
• on energy

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Future Work

• Accept any number of protein sequences as input.
• Determine the probability of any of the input
  protein sequences docking together.

Nick