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SCAI. Activities in the - GRID-field - Molecular Modelling field Possible contribution. GRID-Activities. EGEE-2 SA1: setup and management of the Regional Operations Center for DE/CH (FZK, CSCS, Desy,GSI,SCAI) NA4: support of applications for Biomed and Earth Science (together with DKRZ)

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Presentation Transcript
slide1
SCAI
  • Activities in the
  • - GRID-field
  • - Molecular Modelling field
  • Possible contribution
grid activities
GRID-Activities
  • EGEE-2
      • SA1: setup and management of the Regional Operations Center for DE/CH (FZK, CSCS, Desy,GSI,SCAI)
      • NA4: support of applications for Biomed and Earth Science (together with DKRZ)
    • ressource center providing a production cluster and a preproduction system (PPS)
    • maintainance of different services for the swiss/german community and operation for the DE/CH-VO (VOMS, RB, etc)
  • WISDOM: input preparation and analysis of results
  • deployment of test applications starting with the workflow described below using the UNICORE middleware
  • ….
mm activities docking md

binding affinities

ligands

proteins

MM-activities: Docking & MD

docking

ligand

db

PDB

  • Docking:
  • rough scoring
  • generate starting structure
  • MD:
  • detailed energy function
  • allow receptor flexibility

MD

Hoffmann et al, J.Med.Chem.1999, 42, 4422-4433

workflow procedural details
Workflow: procedural details
  • assignment of partial charges (Gasteiger or AM1-BCC)
  • minimization of ligands previous to docking (optional)
  • docking
  • reranking of docking predictions by minimization of FF energy
  • removing redundant predictions
  • restricting subsequent steps to best candidates
  • perform MD with continuum solvent model or explicit water molecules
    • minimize starting structure
    • heating
    • equilibration
    • production run
  • analyse MD-run (to be integrated)

J

preliminary results
Preliminary results

Quality of predictions:

correlation with exp. affinities / rms (quality of placements)

possible contributions
Possible contributions
  • GRID aspects
    • Transfer of the existing UNICORE workflow to gLite
      • special problem: workflow control and distributed data management
      • strategy:
        • develop prototypic storage of process data in database
        • transfer prototype to gLite
  • Modelling aspects
    • Input preparation
    • potentially result analysis