Automatically Recognize Which Chains Are From Protein And Which Chains From Ligands

Question

[ajingnk]

If I read a PDB file, is there any tool we can use to recognize which chainID is for protein, which is for ligands and which is other addictives?

Thanks

Answer 1

[João Rodrigues]

If you can query the RCSB website, they have nice REST web services that can tell you this: example 1, example 2.

Another alternative, worse, is to compile a list of amino acid residue names (including modifications) and then cross-check with your protein chains.

Finally, you can download the chemical components dictionary and use this to parse your structure.

[ajingnk]

So RCSB REST web services provide information which is not included in their PDB file?

[João Rodrigues]

Short answer: yes. Mostly because the PDB file is rarely filled decently by the authors (i.e. all accession numbers, etc).

Answer 2

[Woa]

I guess if the molecule is a protein there will be a sequence description in the PDB file. So search for those ChainIDs which don't have sequence descriptions. However some small peptide ligand can have sequence too.

Look into PDBSUM database, mostlikely you'll find which ChainID corresponds to the macromolecule or ligand

However I'm not sure whether you'll be able to distinguish ligands from additives by both of these ways.

Alternatively, try http://www.bindingmoad.org/ which distinguishes ligands from general additives for a lot of PDB structures.

Answer 3

[Vladimir Chupakhin]

Go with BioPython, this library have very nice PDB functionality.