An Automated Protein Sequence to Protein iNteraction Generator

1

• An Automated Protein Sequence to Protein
  iNteraction Generator
• it does Things with Stuff.
• UNR Center for Bioinformatics
• Advisor Brian Beck

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Proteins What are they?

• Little machines that carry out small tasks
  (functions)
• Many work together iNteract
• These small tasks add to large tasks
• Digestion
• Blood pressure
• Everything
• Staying alive

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Imagine a Car

• Many little pieces (proteins) that each do a
  small task
• Rotate lever
• Turn that other thing-a-ma-bob
• All work together iNteract to do a larger task
• Drive the car

• Mechanic vs. Scientist

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Now an organism So many interactions!
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Interactionsand Logic

• If we know how and/or if a group of proteins
  interacthelps us figure out what task is going
  on
• If we know all of these little tasks, we begin to
  understand how an organism works gtresearchers
  main goal 1
• If we know how it all works, we can change the
  organism by changing some proteins function
• A.K.A Drug Development gt researchers main goal
  2
• Modify a part in your car to make it work better

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AutomN Background

• AutomN
• Is software ( new methods)
• Speeds up research (automatic point and click)
• Make it easy as possible so almost anyone can use
  it
• Solve computer nightmares file formats! Aghhh!
• Is easy to change (no programming necessary)
• Is extensible not just for proteins
• Main Research goals for this class
• Take a set of proteins in any computer format and
  see if / how they interact only using a computer

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Future Work

• Expand AutomN to do computations on things other
  than proteins
• More support for other computer types
• Debug! Debug! Debug!
• Make it run parts of itself on other computers
• Make it work on a supercomputer

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Conclusions

• Drug development better understand organisms
• Cut research time
• Easy to use ? good teaching tool