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

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 http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/c 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

11. 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

12. Results NoprocProc evalTime(hrs)Speedup 1173.221 2241.301.8 4324.223 76135.6 14136.1511.9 26253.5620.5 5150236.6 1011001.1663

13. References STALK http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/docking.htmlhttp://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/docking.html PGAPack http://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/pgapack.htmlhttp://www.fp.mcs.anl.gov/ccst/research/reports_pre1998/comp_bio/stal k/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/bioinfo rmatikI/materialien/PL-Docking.pdfhttp://www.zbi.unisaarland.de/zbi/stud/lehrveranstaltungen/ws01/bioinfo rmatikI/materialien/PL-Docking.pdf http://archive.ncsa.uiuc.edu/General/Training/SC95/GII.Apps3.html