Overview

POSIT works best when fitting to a collection of co-crystal ligands, however, it can be used for a single ligand targets. Each pose that POSIT generates is analyzed with a simple heuristic and marked with a probability (seen below).

The structures output by POSIT are annotated with information about the best-fit receptor and with various metrics describing the details of the pose. These details are stored in SDDATA and can be viewed with most molecular structure viewers.

The details are as follows:

Name Description
Docking Input Order The input order from the original file
Result GREAT, GOOD, MEDIOCRE or POOR detailing the quality of the result
POSIT receptor title the name of the receptor (taken from the original protein)
POSIT receptor filename the filename of the original receptor
POSIT::Probability Estimated probability of being within 2 Ångström RMSD of the real structure (assuming binding)
POSIT::Method The underlying method used (SHAPEFIT, HYBRID, FRED)
Dock Type The docking type used (which is POSIT in this case)

These values are also written to the report file in a tab separated format, see -prefix for details.

The probability that the computed pose is a correct pose is generated as described in Predicting the Quality of the Pose.

The values in the Result field are as follows:

Result Meaning
GREAT Computed pose is likely (75%-100%) probability) to be within 2.0 Å of experimentally-derived pose.
GOOD Computed pose may be (50%-75%) probability) to be within 2.0 Å of experimentally-derived pose.
MEDIOCRE Take with a grain of salt (33%-50%) probability)
POOR Take with a huge grain of salt (<33% probability)

By default, POOR poses are not written out, they are rejected as unsuitable. The number of rejected molecules is recorded in the status file.