Glide docking
Glide in 2017-2 release
For similarity suite, select similarity score better than 0.5
For glide docking, using the Refine only protocol
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.
No
Sybyl Simularity Suite, Glide
Sybyl X-1.3, Glide in Schrodinger 2017-2 Release
Assumed pH 3:7
Tautomers considered
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.
For similarity suite, select similarity score better than 0.5
For glide docking, using the Refine only protocol
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.
No
Yes