This week a bioinformatics PhD candidate was talking about his PDB analysis tool which was aimed at studying protein-ligand statistics and asked for some advice on what should he consider as "biologically relevant" or not. I told him many of the most common molecules he found were buffers, cryoprotectants, metals used for phasing, etc., and also said that some cases could be more complicated (e.g., PO4 is very common because of its use as a buffer, but in the same time it could be biologically relevant in many cases such as kinases or phosphatases).
Well, I tried my best to list most "usually biologically irrelevant" I could remember, but now I wonder if that is something someone has probably thought about doing before and there's some article/database dealing with it somewhere. Any suggestions? Lucas
