Detecting Terminals In Protein Structures

Question

[Reyhaneh]

Hi

I want to detect C-terminals and N-terminals in a set of protein PDB files. The loop structure (with no helical/sheet secondary structure) at start of the structure can be counted as N-terminal and similarly the loop region at end for C-terminal. But the problem is that these loops are not always terminus but can be a loop section connecting the protein to another domain which has been chopped off in the PDB. or they can be a extension of a alpha- helices.

Using the protein PDB files how can I detect if these loops (at start/end) are actual terminals?

Thank you in advance

Answer 1

[andreas.prlic]

You could look at the SEQRES residues and see how they related to the ATOM records. However that can sometimes still give you only parts of a sequence. You probably want to look at how the PDB entry maps to uniprot. You could do this for single files using the Protein Feature View, or if you want to script this, parse the SIFTS Uniprot to PDB mapping files.