In the work panel, click on the LIGAND button to add a ligand of interest. This is mandatory.
Add amino acids by clicking on the buttons AMINO ACID and ANY AMINO as you like. You must add at least one of these obligatorily.
Connect all the components that you added to the panel using the buttons DISTANCE, GAP and NEXT.
Click on DISTANCE to associate two components according to their proximity measured in angstroms (Å). Default range of distance is [0.5, 7.0]. You can modify this range doing double-click on the red lines. You have to use this association to connect the ligand and one amino acid obligatorily.
Click on GAP to define the direction of two amino acids according to the sequence of the chain of amino acids inside of the biomacromolecule.
Click on NEXT to associate two amino acids according to the sequence of the chain of amino acids inside of the biomacromolecule.
After you have designed the structural pattern correctly, click on the SEARCH button and the application will start looking for coincidences of your pattern in PDB.
Observe the results of the search shown individually in the results section. You can analyze the structure of each coincidence in the 3D viewer by clicking the 3D buttons.
