DUMM6

Attendees & Time

Sarah, Michael M, Ryan, Magdalena, Peter, Kong, Jens, Dahlia, John

Date: April 2nd, 2010. 1:05 pm.

Slides

1. Philosophy

• deleted unused things
• cleaned up code
• streamlined call graph
• single mode gone (use version 3.5.54.70)
• contact scoring gone
• precalculate various grid terms

2. DOCK 3.5.54.72 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 (use dock.csh instead of calling directly)
• speedups (3-5x)

3. 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

4. New keywords

• keyword default suggested
• remove_positive_solvation no YES
• check_clashes yes YES

5. DISI

• it is great

All of this is live since Mar 18 2010 in dock72!

Requests/Improvements

Sarah 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?

Action Items

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