Release Notes

POSIT v3.1.0

June 2014

Major Features

  • The HYBRID and FRED algorithms have been incorporated into POSIT, the appropriate method is determined by analyzing the ligand to pose against the input receptors.
  • Multiprocessing has been enabled through the use of MPI, to speed calculations.
  • POSIT now supports a list of receptors files or .lst file as input. This overcomes command-line limitations for the number of receptors that can be used simultaneously.
  • Added a MEDIOCRE result rating for results between 33% and 50% probability.
  • Command line parameters have been simplified and updated to be compatible with the OEDocking Suite of tools. The following command-line options have been removed, see the documentation for full details.
    • outcomplexes
    • outreceptors
    • clashcomplexes
    • clashreceptors
    • alternatePoses
    • cleanupWithProtein
    • mcs
    • minInitialProbability
    • minInitialTanimotoCombo
    • minTanimotoCombo
    • probabilityStop
    • scatter
    • selectReceptorBy
    • strain

Major Bug Fixes

  • POSIT no longer automatically strips out incoming SDData fields.

Minor Bug Fixes

  • The default for the option -ignore_nitrogen_stereo has been changed to true to account for the nature of time-averaged crystallographic structures.

POSIT v1.0.3

September 2012

Major Bug Fixes

  • Stereo isomer detection was not handling bridgeheads properly, this caused some non-stereo molecules to be identified as such.

POSIT v1.0.2

July 2012

Major Features

  • The optimizer has been enhanced to produce better aligned structures in certain cases.

Major Bug Fixes

  • A memory leak in the optimizer has been fixed, POSIT now properly handles large streams of molecules.
  • The -mcs flag has been turned off by default. In some cases, the mcs was taking far too long for no real benefit in pose prediction.

POSIT v1.0.1

February 2012

Major Bug Fixes

  • In some rare cases the -mcs flag could cause a portion of the posed ligand to be fixed in space while the rest was optimized correctly, this causes very bad geometry molecules that can score very well. POSIT has been fixed to optimize the whole molecule in such cases.

Minor Bug Fixes

  • The version numbers for make_pose_receptor and combine_receptors were being incorrectly output in the OpenEye Banner, this has been updated to reflect the correct POSIT version.

Minor Features

  • -outputall flag has been added to send all computed output to the file specified by -out, -outcomplexes or -outreceptors. It as a shortcut for:

    -minInitialTanimotoCombo 0.0 -minTanimotoCombo 0.0 -minProbability 0.0 \
      -allowedClashes allclashes
    
  • if any of the input receptors has a clashing ligand, a warning will be output and POSIT will be set to accept clashes of the same severity as the receptor ligand.

  • POSIT can now stream output specified by the -out switch to stdout using the

    command line switch -out .sdf or -out .oeb

POSIT v1.0.0

November 2011

First release of POSIT.

Traditional structure based pose-prediction has not been very accurate in reproducing crystallographic poses. This can be rectified by using all of the information present in a crystal structure - both ligand and protein structure. POSIT is a flexible docking technique that uses both the known protein and ligand structure to predict poses. Furthermore, using this information generates a probability that the predicted pose is indeed correct. This has far reaching implications for real world lead optimization scenarios including measuring confidence but also the ability to select the existing crystal structure that best predicts the docked pose for a given molecule.

Features

  • Probability based pose-prediction
  • Performs better than structure-based pose-prediction for poses similar to known bound ligands.
  • All-atom optimization of poses based on known bound-ligands and ligand-protein interactions.
  • Fast detection of best known receptor (complex) to determine pose.