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Tools for working with ligand-protein complexes

This section discusses functionality that's available when both a protein, and small molecule are open. This is aimed towards analyzing ligand-protein interactions.

Note that when analyzing protein-ligand complexes, you may with to use the Surface, or Spacefill views for the protein, and/or enable Dim peptide. You may also wish to use the Near sfc button if in sticks or ball and stick mode, to hide internal protein atoms and bonds.

Creating a ligand from hetero atoms

Hetero residues in the protein data, e.g. loaded from an mmCIF file, can be used to load small molecules. To do so, click one of the buttons that appears next to Make ligs: in the protein section of the UI, if this is displayed. This will open a small molecule. You can manipulate it directly, or save to a sdf mol2 or other file on disk.

You can also, in Residue selection mode, select a hetero residue that respresents a ligand, and click Make ligand from res. This can also be used to create molecules from amino acids.

Moving a ligand to the protein

In addition to using the standard movement tools, you can snap the active ligand into a desired position. To do this, with the ligand selected, click one of the Move lig to --- buttons, in the protein section if available. This set of buttons is determined by hetero residues in the protein data. This will attempt to position the molecule atom-for-atom in the correct location. If unable, it will move the ligand in the hetero residue's centroid. Note that you cannot perform MD on the hetero residue directly, but you can on a ligand created from it, or moved to its position.

Measuring potential energy

You can measure the instantaneous potential energy between a ligand positioned near a protein, the protein, and nearby water molecules, e.g. as stabilized by hydrogen bonds. To do so: (todo). This computes energy using similar forces to the non-bonded molecular dynamics ones:

  • Lennard Jones interactions
  • Short-range Coulomb force
  • Long-range reciprocal Coulomb force