STALK

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STALK An Interactive Virtual Molecular Docking
System

• Authors Levine, Facello, Hallstrom, Reeder,
  Walenz, Stevens
• (MCS Division at Argonne National Laboratory)
• Presentation by Amruta Purandare

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Problem Molecular docking

• Computational biology problem applied to
  pharmaceutical industry
• Study of protein drug interactions
• Predicting existence and sites of interactions
• Application developing new drugs
• If a drug interacts with protein ?
• Yes how fast

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Why Genetic Algorithms ?

• Optimization problem
• Goal Minimizing free energy in molecular
  interactions
• 3 D molecules interacting through unidentified
  interfaces
• Strings with 6 parameters
• Search Space Possible conformations analyzed
  for energy

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Solution

• Protein molecule fixed
• Decide parameters for a ligand using rigid body
  formulation
• 3 Translational (x, y, z) 0, A
• 3 Rotational along 3 axes -pi, pi
• E

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Why Parallelism ?

• Overwhelming computational analyses
• 3 D nature of Macromolecules
• Large number of conformations
• Evaluation is cost dominant O(n1,n2)
• Degree of parallelism
• speeds up execution
• helps in trying large variations

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Approach used by the authors

• STALK system for visualization of molecular
  docking
• http//www.fp.mcs.anl.gov/ccst/research/reports_p
  re1998/comp_bio/stalk/docking.html
• Master/Slave, Message Passing using MPI, MIMD
  model
• Subdivision of problem to a cubic cell

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Interactive Model (Non-GA part of STALK)

• Visualization of interactions
• CAVE 10x10x9 feet VR environment
• User Interactive wand, shutter glasses
• Tracking system capture users position,
  orientation

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Experiments

• Protein Ribonuclease S
• Population size 1000
• 100 Strings replaced in each iteration
• Tournament selection
• Uniform crossover (p0.9)
• Mutation (p0.1 rate1/6)
• add/subtract randomly from G µ0 s0.1

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Results
Noproc Proc eval Time(hrs) Speedup
1 1 73.22 1
2 2 41.30 1.8
4 3 24.22 3
7 6 13 5.6
14 13 6.15 11.9
26 25 3.56 20.5
51 50 2 36.6
101 100 1.16 63
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References

• STALK
• http//www.fp.mcs.anl.gov/ccst/research/reports_pr
  e1998/comp_bio/stalk/docking.html
• PGAPack
• http//www.fp.mcs.anl.gov/ccst/research/reports_pr
  e1998/comp_bio/stalk/pgapack.html
• CAVE
• http//cave.ncsa.uiuc.edu/
• Protein Docking
• http//abagyan.scripps.edu/lab/web/man/50.pdf
• http//www.zbi.unisaarland.de/zbi/stud/lehrveranst
  altungen/ws01/bioinformatikI/materialien/PL-Dockin
  g.pdf
• http//archive.ncsa.uiuc.edu/General/Training/SC95
  /GII.Apps3.html

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