D3R-GC3-Scoring-Redocking-Xray-Score
CACTVS Chemoinformatics Toolkit v3.433/Schrödinger Suite 2016-1/Glide/CORINA v3.60/UCSF Chimera v1.10.2
Glide software with the SP protocol and constraints on the common substructure with either CatS_15, CatS_20 or CatS_24.
D3R-GC3-Pose-Redocking-Xray-Score
CACTVS Chemoinformatics Toolkit v3.433/Schrödinger Suite 2016-1/Glide/CORINA v3.60/UCSF Chimera v1.10.2
Protonation state of ligands at pH 7.0+/-1 was considered.
The protein 'qjan' from the complex with CatS_15 was used for docking. Protein was prepared (hydrogens added) using the Schrödinger Suite. 3D coordinates of the ligands (MOL2 format) with different protonation states corresponding to a pH of 7.0+/-1 were generated using Schrödinger LigPrep. Binding site was defined as a sphere with 20 Å radius around a virtual point with coordinates (-7,12,-8).
Glide software with the SP protocol and constraints on the common substructure with either CatS_15, CatS_20 or CatS_24.
Docking runs with ligands from the Free Energy Set 1 were executed using Glide software with the SP protocol, and default values, except the constraints applied on the common substructure with either CatS_15, CatS_20 or CatS_24. The poses with the best docking score were selected for submission (1 pose per compound). Protein structures were converted into PDB format for submission using UCSF Chimera, and the docking poses were converted into MOL format using CORINA (the MOL format corresponds to the SDF output format in CORINA).
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