The Ligand Optimizer

The Ligand Optimizer (Image lead_optimizer_16_n_p) makes it possible to modify small molecules while taking the surrounding protein environment into account.

It can be used when a specific binding mode is already known (for instance from a docking simulation, or from a co-crystallized ligand) to investigate how changes in the ligand chemistry will affect the binding. It is also possible to use the Ligand Optimizer without any protein context, for instance in order to prepare small molecules before a docking simulation.

To invoke the Ligand Optimizer dialog, select a single ligand or docking result from the Project Tree and click the Ligand Optimizer button in the Structure tools panel below the Project Tree. It is possible to convert molecules from other categories to ligand (see Converting molecules to Cofactors or Ligands).

Note: Whenever a change is performed on the ligand, all atomic charges are cleared and reassigned using built-in preparation. Likewise, some chemical groups (such as carboxylate) are automatically turned into a delocalized bond representation when recognized.

Also note: It is possible to undo and redo operations done while using the dialog. If the dialog is canceled, all changes done are rolled back.

The Ligand Optimizer dialog is composed of the following five panels:


Subsections