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Ligand design in the new interface with a single hydrogen atom selected.

Ligand design is a key feature of Small molecule design puzzles. The term small molecule is used interchangeably with ligand.

In the original interface, ligand design is available as a mode. In the selection interface and the new interface, ligand design appears as a tool in the action bar.

There are specific View Options for working with ligands. There's "Ligand Specific" coloring option and "Binding Site" and "Cartoon Ligand" protein views. The X-ray tunnel for ligand ligand option may also make the ligand easier to see. The "Show Bonds (non-protein)" option shows hydrogen bonds between the ligand and the protein, a key design feature.

The ligand view options use CPK colors. Hydrogen atoms are shown as white caps, nitrogen atoms are blue, and oxygen atoms are red. Carbon atoms are shown in a default color, which can be changed. Other atoms have their CPK colors, such as yellow for sulfur, but it can be difficult to distinguish them.

The ligand design panel has the following sections

  1. Atom Selection or Fragment Selection
  2. Bond Selection (when the Atom Selection view is active)
  3. button to switch between atom and fragment selection views
  4. Cleanup Structure

The general functions of the ligand design panel include:

  • adding an atom or fragment
  • changing an atom to a different element
  • deleting an atom
  • changing single, double, or triple bonds
  • deleting a bond
  • clearing an atom selection

In both the original and selection interfaces, ligand design depends on atoms being selected. In both interfaces, clicking on atoms of the ligand selects them. (In the selection interface, the ligand itself must first be selected as a segment selection.)

Multiple atoms can be selected by clicking on them. In the original interface, a "broom" icon clears the selected atoms. In the selection interface, clicking on the background clears the selected atoms and deselects the ligand. The ligand must be re-selected and the ligand design tool opened again to proceed in the selection interface.

The ligand design options available depend on the atom selected, including what chemical element it is and it's bonding relationship to other atoms. Options that aren't currently available are "grayed out".

Changing a bond requires selecting two adjacent non-hydrogen heavy atoms. The possible bonds between heavy atoms are:

  • single
  • double
  • triple

For the 2017 version of ligand design, the ligand design cheat sheet developed by the Foldit science team summarized the features available in ligand design. The implementation is different in the 2021 version, but the basic concepts are the same.