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STALK – An Interactive Virtual Molecular Docking System

STALK – An Interactive Virtual Molecular Docking System. Authors – Levine, Facello, Hallstrom, Reeder, Walenz, Stevens ( MCS Division at Argonne National Laboratory ) Presentation by Amruta Purandare. Problem – Molecular docking.

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STALK – An Interactive Virtual Molecular Docking System

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  1. STALK – An Interactive Virtual Molecular Docking System Authors – Levine, Facello, Hallstrom, Reeder, Walenz, Stevens (MCS Division at Argonne National Laboratory) Presentation by Amruta Purandare

  2. 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

  3. 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

  4. 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 =

  5. 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

  6. Approach used by the authors • STALK – system for visualization of molecular docking http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stalk/docking.html • Master/Slave, Message Passing using MPI, MIMD model • Subdivision of problem to a cubic cell

  7. Interactive Model (Non-GA part of STALK) • Visualization of interactions • CAVE 10x10x9 feet VR environment • User Interactive – wand, shutter glasses • Tracking system – capture user’s position, orientation

  8. Experiments • Protein – Ribonuclease S • Population size = 1000 • 100 Strings replaced in each iteration • Tournament selection • Uniform crossover (p=0.9) • Mutation (p=0.1 rate=1/6) • add/subtract randomly from G μ=0 σ=0.1

  9. Results

  10. References • STALK • http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stalk/docking.html • PGAPack • http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/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/lehrveranstaltungen/ws01/bioinformatikI/materialien/PL-Docking.pdf • http://archive.ncsa.uiuc.edu/General/Training/SC95/GII.Apps3.html

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