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SCAI

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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SCAI

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  1. SCAI • Activities in the • - GRID-field • - Molecular Modelling field • Possible contribution

  2. 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 • ….

  3. 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

  4. 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

  5. Preliminary results Quality of predictions: correlation with exp. affinities / rms (quality of placements)

  6. 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

  7. Thank you!

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