Protocols are procedural lego bricks to carry out some manipulation or series of manipulations involved in or peripheral to ligand discovery. They are different from tutorials, which are thematic and project-oriented, and typically may call upon one or more protocols.
Before docking
== Protocol B1:
Protocol B2: Assemble a list of decoys
Protocol B3: Prepare a ligand for docking
Protocol B4: Prepare a list of N random molecules
Protocol B5: Generate 3D representations of molecules from SMILES
Protocol B6:
Docking
Protocol D1: Dock a single ligand to a single target
After docking
Protocol A1: Cluster molecules
Protocol A2: Purchase compounds
Unrelated to docking
Protocol U1: similarity searching
Protocol U2: generate 2D depiction from SMILES
Protocol U3: xxx