Understanding MakeDOCK, which automates sphere and grid generation: Difference between revisions
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=== | === What is MakeDOCK? === | ||
* MakeDOCK automates the process of sphere and grid generation for a target. | * MakeDOCK automates the process of sphere and grid generation for a target. | ||
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=== Receptor Preparation === | === Receptor Preparation === | ||
To prepare a typical pdb structure for receptor | To prepare a typical pdb structure for use as the receptor in MakeDOCK, perform the following steps: | ||
# Remove solvent (i.e. crystallographic waters) | # Remove solvent (i.e. crystallographic waters) | ||
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# Delete all hydrogen atoms | # Delete all hydrogen atoms | ||
# Save as rec_original.pdb | # Save as rec_original.pdb | ||
=== Ligand Preparations === | |||
To prepare the ligand specification, reload the original pdb structure and perform the following steps: | |||
# Delete everything BUT the ligand atoms | |||
# Add hydrogens and charges | |||
Revision as of 00:28, 11 September 2007
What is MakeDOCK?
- MakeDOCK automates the process of sphere and grid generation for a target.
Input files to MakeDOCK
- The following files are required to specify the target for MakeDOCK:
- rec.pdb: Prepared receptor file
- xtal-lig.mol2 (or .pdb): Ligand specification file
Receptor Preparation
To prepare a typical pdb structure for use as the receptor in MakeDOCK, perform the following steps:
- Remove solvent (i.e. crystallographic waters)
- Remove other non-essential hetero-atoms (everything but perhaps a co-factor essential for ligand binding)
- Remove the ligand itself
- Delete all hydrogen atoms
- Save as rec_original.pdb
Ligand Preparations
To prepare the ligand specification, reload the original pdb structure and perform the following steps:
- Delete everything BUT the ligand atoms
- Add hydrogens and charges