ValLigURL: ligand-structure Comparision and Validation
The web-based tool ValLigURL, which is totally pronounced Valley Girl (serious, check the pdf) allows a crystallographer to compare and validate ligands in the PDB.
This server provides a way to examine whether the ligand in a structure has been seen in a particular conformation. The great part is that this server allows you to upload your own structure for a comparison against existing structures. The server takes about a minute to run.
This could be helpful if you are trying to determine whether you have kissing waters, crystallization remnant or your ligand of interest.
The following is a JMOL output (one option) of a search ligand (thick lines) verse the ligand (thin lines) from MSDchem.
Finally, the server can be used by structural bioinformaticians to examine conformational diversity and quality for one or more ligands in the PDB. In other words, this server is hella sweet.