AGFR tutorials

Step-by-step tutorials with the AGFR graphical interface.

Before you start:

For command-line examples see the AutoDockFR tutorials.

Docking box around a known ligand

Docking box from a known ligand

CDK2 (PDB 4EK3) with a ligand from 4EK4. Also shows the equivalent command line.

Docking box around AutoSite fill points

Docking box from an AutoSite pocket

No ligand known: let AutoSite find pockets and size the box on the best one.

Docking box around selected residues

Docking box from binding-site residues

Define the box from the amino acids that line the active site.

Flexible receptor side chains

Maps for flexible receptor side chains

Make LYS33, LYS88 and LYS89 of CDK2 flexible and adjust the box to cover them.

Covalent ligand outlined with dashed lines

Maps for covalent docking

Prepare PDB 3C9W for docking covalent ligands bound to CYS164.

Affinity map shown as an orthoslice

Visualizing affinity maps

Show maps of a target file as isocontours and orthoslices.

Back to top