Hmm, this makes me think of how upon deposition to the PDB, we describe the expected biological assembly that a crystal structure represents. This is a judgement call, but can be backed up with experimental data. A similar flag for physiological ligands as opposed to components of the crystallization solution (with just as much subjectivity) could be very useful for differentiating physiological versus artifactual ligands. Of course, much easier said than done.
Shane Caldwell McGill University On Thu, Jun 11, 2015 at 3:14 PM, Lucas <lucasbleic...@gmail.com> wrote: > 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 >
