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