Introduction

DOCK addresses the problem of “docking” molecules to each other. In general, “docking” is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. To run the DOCK software on maya, relevant executables are in the directory

[araim1@maya-usr1 ~]$ ls /usr/cluster/dock/6.3/bin/

For example

[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/sphgen
[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/grid
[araim1@maya-usr1 ~]$ /usr/cluster/dock/6.3/bin/dock6

Detailed information about running DOCK can be found in the user’s manual