DOCK Blaster:Protocols: Difference between revisions
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= Before docking = | = Before docking = | ||
== Protocol B1: | == Protocol B1: filtering molecules == | ||
* x | * x | ||
| Line 12: | Line 12: | ||
== Protocol B2: | == Protocol B2: making decoys == | ||
* x | * x | ||
| Line 18: | Line 18: | ||
* z | * z | ||
== Protocol B3: Prepare | == Protocol B3: Prepare ligand for docking == | ||
* x | * x | ||
| Line 24: | Line 24: | ||
* z | * z | ||
== Protocol B4: | == Protocol B4: Get N random molecules == | ||
* x | * x | ||
| Line 30: | Line 30: | ||
* z | * z | ||
== Protocol B5: | == Protocol B5: SMILES to 3D mol2/SDF == | ||
* x | * x | ||
| Line 37: | Line 37: | ||
== Protocol B6: == | == Protocol B6: Autodock pdbqt format== | ||
* x | * x | ||
* y | * y | ||
* z | * 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 = | = Docking = | ||
Revision as of 01:06, 13 February 2009
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
Protocol U1: similarity searching
- x
- y
- z
Protocol U2: generate 2D depiction from SMILES
- x
- y
- z
Protocol U3: xxx
- x
- y
- z