Prime User Manual - ISP

Prime User Manual
Chapter 9: Docking Covalently Bound Ligands
Chapter 9
While Glide is highly efficient at docking ligands that are bound to a receptor through
hydrogen bonds or various nonbonded interactions, it is not able to dock ligands that are
covalently bound to the receptor. Prime provides a covalent docking facility that allows you to
select the attachment point to the receptor and the possible attachment points on the ligand, and
run a Prime loop prediction to find poses for the ligand.
9.1 Running Covalent Docking from Maestro
Covalent docking calculations can be set up and run from the Covalent Docking panel. To open
the Covalent Docking panel, choose Applications > Prime > Covalent Docking in the main
window.
The Covalent Docking panel has two main sections. Above these sections, you can specify the
source of the ligands. In the Ligand reactive groups section, you can specify the kinds of
groups that will react at the receptor attachment site. In the Receptor options section, you can
specify the receptor bond that is broken and choose receptor residues to sample.
9.1.1 Selecting the Ligands
The ligands that you dock to the receptor can be taken from the Project Table or from a file.
• To use the structures that are selected in the Project Table, choose Project Table from the
Use ligands from option menu.
• To read the ligands from a file, choose File from the Use ligands from option menu. You
can then either enter the file name in the Input file text box, or click Browse and navigate
to the file in the file selector that opens. The file must be a Maestro file, and can be compressed
(.maegz, .mae.gz) or uncompressed (.mae).
You should ensure that the structures are all-atom, 3D structures that are properly prepared, for
example by using LigPrep. See the LigPrep User Manual for more information on ligand preparation.
The poses that are returned include both the ligand and the receptor, so you should consider
carefully how many ligands you want to dock.
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