Distinguish Proteins With No Homology Template

Question

[Reyhaneh]

Hi;

I have a list of proteins and between them I want to use docking for those which can not be solved by homology modeling. for example for 1ak4 a homolog template 1m9e exists.

How can I distinguish the proteins which do not have a homolog complex model?

Thanks in advance for your help.

[Spitshine]

Can you rephrase the question? Are you simply looking for proteins without a decent similarity to a protein in the PDB?

[Reyhaneh]

Sorry if the question is misleading. I am looking at some protein complexes on Hwang et al. benchmark (http://zlab.umassmed.edu/benchmark/) and between them I want to choose the complexes which their homolog complex does not exist in PDB.

[Whoknows]

Hi,, you should downlaod PDB proteon list (http://www.rcsb.org/pdb/download/download.do) and then just subtract you list from the PDB list. You may need to blast your query sequences with PDB for finding homolog complex, PDB can perform blast inside, also it gives you whole database sequence for stand-alone blast too.