Question: Automatically Recognize Which Chains Are From Protein And Which Chains From Ligands
1
gravatar for ajingnk
6.9 years ago by
ajingnk130
United States
ajingnk130 wrote:

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

pdb protein • 1.4k views
ADD COMMENTlink modified 6.1 years ago by João Rodrigues2.5k • written 6.9 years ago by ajingnk130
1
gravatar for João Rodrigues
6.1 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

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.

ADD COMMENTlink modified 5 months ago by RamRS27k • written 6.1 years ago by João Rodrigues2.5k

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

ADD REPLYlink written 5.8 years ago by ajingnk130

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

ADD REPLYlink written 5.8 years ago by João Rodrigues2.5k
0
gravatar for Woa
6.9 years ago by
Woa2.8k
United States
Woa2.8k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Woa2.8k
0
gravatar for Vladimir Chupakhin
6.1 years ago by
Toledo, Spain
Vladimir Chupakhin520 wrote:

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

ADD COMMENTlink written 6.1 years ago by Vladimir Chupakhin520
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