Revision as of 17:47, 21 April 2010 by Kolb (Talk)

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Attendees & Time

Date: April 2nd, 2010. 105 pm.


  1. Philosophy
    • deleted unused things
    • cleaned up code
    • streamlined call graph
      • single mode gone (use version
      • contact scoring gone
      • precalculate various grid terms
  1. DOCK improvements
    • chem.bmp bumping instead of distmap contact bumping
    • new hierarchy code (should eliminate some broken)
    • no more out of bounds molecules
    • no more clashing molecules
    • deprecated unused keywords (more later)
    • vdw repulsive term capped at a million (no more overflow bugs with huge negative energies)
    • 64bit/32bit builds (dock.csh instead of calling directly)
    • speedups (3-5x)
  1. Deprecated keywords
    • write_coordinates
    • standard_pdb
    • focus_ratio
    • normalize_save
    • restart_interval
    • mirror_ligands
    • scoring_option
    • mode
    • ligand_type
    • restart
    • output_hydrogens
    • recombine_fragments
    • interpolate
    • ligand_sphere_file
  1. New keywords
    • keyword default suggested
    • remove_positive_solvation no YES
    • check_clashes yes YES
  1. DISI
    • it is great

Hardware updates

Software updates


Sandra raised the issue of the flexible protein code of Niu Huang:

  • Is it compatible with the current improvements? <math>\rightarrow</math> probably not.
  • Is anybody using it?
  • Would it be worth it to update and include it?
  • Can it be used in an automatic fashion, e.g. for DOCK Blaster?
  • How can we predict water positions and usefulness (maybe initial water placement with PLOP)?

<math>\Rightarrow</math> who will be doing all of this?

Database updates



Action Items

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