pose_entropy.py Command Help

Command: $SCHRODINGER/run pose_entropy.py

usage: pose_entropy.py [-v] [-h] [-distance <distance cutoff>]
                       [-eproperty <energy property>] [-probability]
                       [-top-each-cluster]
                       infile outfile

Computes a modified docking score based on work by A.M. Ruvinsky using the
number of poses within each energy well. Poses are first clustered and then
the entropy is computed for each cluster. Input poses should come from Glide
saving 100 poses per ligand. The criteria for duplicate pose elimination
should be reduced to zero (in the Clustering section under Advanced options in
the Output tab of the Glide Docking panel) in order to ensure a full sampling
of each energy well.

This idea was first published by A.M. Ruvinsky in J. Comp. Chem., 26 (11), 2005
"New and Fast Statistical-Thermodynamic Method for Computation of
Protein-Ligand Binding Entropy Substantially Improves Docking Accuracy"

The basic idea is that more poses will be found in energy basins that are
broader, and thus a favorable entropy correction should be applied. In our
implementation we have the standard correction by Ruvinsky based solely on the
number of poses in each basin. We also have an option to weight each pose
probabilistically based on the energy relative to the lowest energy member of
the cluster. The energy basins are computed by clustering all poses for each
ligand based on their RMSD.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  infile                Input Maestro file. Can also be a pose viewer file.
  outfile               Output Maestro file.

options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -distance <distance cutoff>
                        Sets distance at which clustering operation will end.
                        Default=1.0
  -eproperty <energy property>
                        Determines which Glide energy property forms the basis
                        for the entropy calculation. This must be one of the
                        following: emodel (default), cvdw, gscore
                        (GlideScore), dockingscore (Docking Score)
  -probability          Use the energies to determine the probability of
                        occurrence for a given pose in a cluster. Note that
                        Ruvinsky does not do this in his original work.
                        Default=False
  -top-each-cluster     Output the top scoring pose for each cluster of poses
                        for each ligand instead of only the overall top
                        scoring pose for each ligand.