DOCK Blaster:Protocols

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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: filtering molecules

  • x
  • y
  • z


Protocol B2: making decoys

  • x
  • y
  • z

Protocol B3: Prepare ligand for docking

  • x
  • y
  • z

Protocol B4: Get N random molecules

  • x
  • y
  • z

Protocol B5: SMILES to 3D mol2/SDF

  • x
  • y
  • z


Protocol B6: Autodock pdbqt format

  • x
  • y
  • z

Protocol B7: Clustering ligands

  • x
  • y
  • z

Protocol B8: protonate receptor

  • x
  • y
  • z

Protocol B9: search supplier catalogs (pre filtering)

  • x
  • y
  • z

Protocol B10: identify aggregators

  • x
  • y
  • z

Protocol B11: exhaustive search

  • x
  • y
  • z

Protocol B12: make a database subset

  • x
  • y
  • z

Protocol B13: xxx

  • x
  • y
  • z


Docking

Protocol D1: Dock a single ligand to a single target

  • x
  • y
  • z


After docking

Protocol A1: Cluster molecules

  • x
  • y
  • z

Protocol A2: Purchase compounds

  • x
  • y
  • z


Unrelated to docking

Protocol U1: similarity searching

  • x
  • y
  • z


Protocol U2: generate 2D depiction from SMILES

  • x
  • y
  • z

Protocol U3: xxx

  • x
  • y
  • z