1479-1-n5em3-PosePredictionProtocol-S.txt

Name

Data-driven deep learning docking/Schrodinger

Software

Schrodinger/In-house Deep Learning

System Preparation Parameters

Assumed pH 5.0
Tautomers considered
Gasteiger charges

System Preparation Method

Proteins and Ligands were prepared by Maestro's prepwizard with default parameters.
Ligand conformational libraries were generated using ConfGen in Schrodinger.

Pose Prediction Parameters

num_conformers=200

Pose Prediction Method

Poses were ranked by in-house deep learning score. Pose with the highest score were chosen.

Answer 1

No

Answer 2

No

1479-2-z78u0-LigandScoringProtocol-S.txt

Name

Deep Learning Package

Software

AG/DG/TDL-BP/Schrodinger

Parameters

Use AG, DG-GL and/or TDL-BP with default parameters
Use PDBBind as the training data for these models

Method

The features generated by Algebraic Graph, Differential geometry, and Algebraic topology scores are utilized in in-house design neural network models to predict the binding free energy

Answer 1

No

Answer 2

Yes