phfin-PosePredictionProtocol.txt

Name

FlexAID∆S

Software

OpenBabel v2.4 / FlexAID∆S / NRGsuite

System Preparation Parameters

Assumed pH 7.0
Gasteiger charges

System Preparation Method

Ligands' 3D structure were generated using OpenBabel v.2.4 at pH 7.0 with Gasteiger charges. Process_Ligand (distributed with FlexAID and/or the NRGsuite) was used to process both the target and the ligand 3D structures as input to FlexAID. The Binding Site was defined using the GetCleft cavity detection tool (within the NRGsuite or available through biophys.umontreal.ca/nrg)

Pose Prediction Parameters

Genetic Algorithm Generations=2000
Genetic Algorithm Chromosomes=2000
Temperature=14
All flexible bonds of the ligands were fully considered

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. The top 5 poses returned from the FlexAID∆S docking method are submitted with this protocol.

Answer 1

No

Answer 2

No