pcy3r-FreeEnergyProtocol.txt

Name

Glide docking

Software

Glide in 2017-2 release

Parameters

For similarity suite, select similarity score better than 0.5
For glide docking, using the Refine only protocol

Method

System Preparation Method: Openbabel was used for generating 3D structures in pdb format of the ligands from their smile format.
3D structures were generated through 3D structure alignment to a set of templates using the similarity suite of Sybyl X-1.3;
then the outputs were submitted to Glide docking.

Answer 1

No

pcy3r-PosePredictionProtocol.txt

Name

Sybyl Simularity Suite, Glide

Software

Sybyl X-1.3, Glide in Schrodinger 2017-2 Release

System Preparation Parameters

Assumed pH 3:7
Tautomers considered

System Preparation Method

Openbabel was used for generating 3D structures in pdb format of the ligands from their smile format.
3D structures were generated through 3D structure alignment to a set of templates using the similarity suite of Sybyl X-1.3;
then the outputs were submitted to Glide docking.

Pose Prediction Parameters

For similarity suite, select similarity score better than 0.5
For glide docking, using the Refine only protocol

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 from the Vina docking are submitted with this protocol.

Answer 1

No

Answer 2

Yes