Name

stage2_vinardo_score

Software

smina

Parameters

--exhaustiveness 50 --seed 0

Method

This uses the vinardo scoring function built into smina.
vinardo was used to minimize vina-generated poses (the exact same pose-set
used in other protocols) and the resulting best affinity was used as
the prediction.

Comparing this protocol to the stage2_vina_score protocol will give some
indication if vinardo is better at affinity prediction, independent of
the sampling algorithm (that's not really true - you can't fully
separate sampling from scoring).

Name

stage2_vinardo_score

Software

smina

System Preparation Parameters

This field intentionally left blank, but not really since the validator won't accept a blank field.

System Preparation Method

Waters were stripped from receptors. Protonation was performed with openbabel.

Pose Prediction Parameters

--exhaustiveness 50 --seed 0

Pose Prediction Method

smina was used to dock to a selection of reference
receptors (same poses as stage1) and to re-dock the provided stage2 complexes.
A minimized pose generate from the crystal pose was generated as well.
All pose generate was done using the default Autodock Vina scoring function.