[Dock-fans] ANNOUNCING: Release of DOCK 5.3.0

DOCK dock_bugs at dock.compbio.ucsf.edu
Thu Nov 3 17:29:14 PST 2005

Dear DOCK Fans,      

        We are pleased to announce the official release of DOCK version 
5.3.0, which includes additional functionality and a number of bug fixes 
(see below for more information).  If you would like to download the new 
version, go to the following link for instructions:


Your Login and Password are the same as for version 5.2.0.  As before, 
you will be given FIVE opportunities to download DOCK, at which time the 
password will expire. 

Documentation and tutorials for this release can be found  at 

Thank you for your continued interest in DOCK.  We hope this software 
continues to be a useful part of your design efforts.

The DOCK Team



_DOCK Functionality_ 

/POSE CLUSTERING/:  Clustering is often required as part of post-dock 
processing.  With this new function, dock is run and the scored poses 
are clustered based on RMSD and rank.  The best scoring pose in each of 
the clusters is then printed.

_Bug Fixes_

Several critical bugs have been identified and fixed since the last 
release. These bugs include:

/For DOCK/:

    * VDW and es components of scoring function can now be scaled
    * Conformations that extend beyond the edge of the grid are skipped
    * Switch between rigid and flexible docking options works smoothly
    * Time for runs is calculated properly on all platforms
    * If an orientation cannot be generated or if a pose cannot be
      scored, an error is now thrown
    * Sphgen files containing more than one cluster are processed properly
    * If maximum number of ligands to be docked is set, the correct
      count it reported

/For DOCK in parallel/:

    * If only one processor is specified, calculation reverts to
      non-parallel behavior
    * Command-line flags from mpi runs are parsed correctly
    * Mpi runs stop properly at maximum number of ligands, if the flag
      is set

/For the Accessory programs:/

    * SPHGEN clusters properly on all platforms
    * NCHEMGRID_GB and NCHEMGRID_SA calculate grid values properly on
      all platforms

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