1146-1-mubj7-MeilerLabBCL_GC4_Task1a_Protocol_PosePrediction_1b.txt

Name

BCL::MolAlign with protein-ligand complex energy minimization

Software

BCL v3.5, corina v4.1.0, MOE 2018.01

System Preparation Parameters

Molecules prepared as in "BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping" (in review). Energy minimization performed in MOE using the Amber ff14SB forcefield with EHT parameters for ligands. Default parameters for minimization were employed.

System Preparation Method

Molecules prepared as in "BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping" (in review).

Pose Prediction Parameters

Best pose predicted from the best BCL::MolAlign property distance score was energy-minimized.

Pose Prediction Method

Crystallographic protein-ligand complexes of BACE-1 with inhibitors were obtained from the PDB. Ligands were clustered according to chemical descriptors as reported in doi: 10.1007/s10822-016-9895-2 and doi: 10.1007/s10822-015-9893-9. Target compounds were assigned a cluster based on chemical similarity, and we implemented BCL::MolAlign to structurally align target compounds to template scaffolds within their clusters. The best ligand pose by alignment score was energy-minimized in PDB ID 5YGX.

Answer 1

Yes

Answer 2

No