I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer.
In a heterodimer there are two chains in which there are some residues between monomers which take part in the interaction of monomers and building the structure of heterodimer, and there are other residues interacting inside each monomer for building the structure of that monomer. There are some PDB IDs related to heterodimers in PDB.
Now imagine that we are trying to show which residues are physically interacting between two monomers in a heterodimer, and then we are trying two show the site of these physically interacting residues in the sequence related to that special structure. For that, we need to find the sequence related to that structure and we can download it from PDB.
But if we want to make a multiple sequence alignment of that sequence, first we need to find the refseq sequence of that and then we must blast the sequence and find homologues of that sequence.
Here there are some challenges:
- we must find residues interacting in the structure of heterodimer between two monomers.
- we must find the sequences of monomer chains of the heterodimer and map the interacting residues in the structure to the sequence.
- we know that when a structure is solved and its monomers are sequenced, may be they are not able to completely sequence the heterodimer and residue numbers are maybe different from the related refseq sequence.
I would like to know how can we find the related refseq sequence (or sequences, in the case of heterodimer) and then how can we map the physically interacting residues in the structure of PDB ID to refseq sequence (finding the sites of these interacting residues in that refseq sequence) regarding three challenges mentioned above.
Imagine that I have 100 PDB IDs of 100 nonredundant heterodimers and I would like to find and download the structures, sequence and finally refseq sequence. What should I do?