1 / 14

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.

max
Télécharger la présentation

STALK – An Interactive Virtual Molecular Docking System

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related