Searching for a specific ligand conformation?
More specifically, the rotational state of an amide (cis or trans, relative to a known atom)… ValLigURL almost (but not quite) does what you want. Upload your ligand and it will retrieve all the copies of the same ligand from the pdb, superimpose them on yours, and report the results. By reducing the atoms in the search ligand to a set including just a single dihedral, and unchecking “Ignore ligands with different number of atoms,” you can sort by RMS to find just what you are looking for.
