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STALK – An Interactive Virtual Molecular Docking System Authors – Levine, Facello, Hallstrom, Reeder, Walenz, Stevens ( MCS Division at Argonne National.

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Presentation on theme: "STALK – An Interactive Virtual Molecular Docking System Authors – Levine, Facello, Hallstrom, Reeder, Walenz, Stevens ( MCS Division at Argonne National."— Presentation transcript:

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

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5 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

6 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 =

7 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

8 Approach used by the authors STALK – system for visualization of molecular docking omp_bio/stalk/docking.html Master/Slave, Message Passing using MPI, MIMD model Subdivision of problem to a cubic cell

9 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

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11 Experiments Protein – Ribonuclease S Population size = 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

12 Results NoprocProc evalTime(hrs)Speedup

13 References STALK k/docking.htmlhttp://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/docking.html PGAPack k/pgapack.htmlhttp://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/pgapack.html CAVE Protein Docking rmatikI/materialien/PL-Docking.pdfhttp://www.zbi.unisaarland.de/zbi/stud/lehrveranstaltungen/ws01/bioinfo rmatikI/materialien/PL-Docking.pdf

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