I have a protein obtained through ab initio modeling. I would like to know whether this protein is exhibiting any kind of structural similarities with other proteins available in the PDB. How I can search this? Can any one suggest me a simple method to select structurally similar proteins from PDB?
You could try 3D blast: http://3d-blast.life.nctu.edu.tw/
Alternately, try the Dali server: http://ekhidna.biocenter.helsinki.fi/dali_server/start
PDBeFold also looks promising, though I've not used it before: http://www.ebi.ac.uk/msd-srv/ssm/
Just wondering: is there necessarily a strong correlation between the structural similarity of two proteins and their roles/uses/properties? I for one would - heuristically - doubt that rather a lot.
It depends upon the direction you examine the correlation. If you take X proteins that look similar, there's no particular reason to imagine they'll have the same function - depending on how exact the match is, I'd estimate no more than half to a quarter of the X you pull out of a database will function similarly to the input. Heck, even close family members sometimes have different functions due to single-residue mutations or the like. But if you take Y proteins that do something similar, there's a reasonably good chance they'll have some significant structural similarities - once nature figures out a way to do some reaction, it tends to go for variations on that theme.
However, since we don't always know all the functions of a protein, so can't always search by that, one can do worse than search by structure, then look up what all the homologous proteins do, and look for functional similarities.
Similarly, one might use a structure similarity search to, say, look for off-targets for a drug one designed, or to try and figure out what cell compartment a protein might localize to, or what its binding partners might be, or simply to identify common secondary structure motifs (say, an ankyrin repeat) that one isn't particularly familiar with, but which is already annotated for a protein that has a structure available.
Thanks William and Michael for the suggestions and useful discussions. I will try these tools.
If you have a pdb file of your structure, then the easiest is to use VAST + from NCBI https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi .
You just enter your RCSB structure code and it will return a list of similar pdb files ranked in order of similarity.
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