Has anyone used the SCOP website? I tried to search for my protein pdb id 3w0f but could not get its classification. Does anybody know how to get around this problem? The website is very user unfriendly.
Try fastSCOP: http://fastscop.life.nctu.edu.tw/dbsas-upload.php
You can upload your protein's structure and it will try to make a SCOP classification. Let me know how it goes!
I forgot to mention that you may get all kinds of lines that look like error messages - Scroll down to the bottom of the page to get the answer.
Your structure just doesn't seem to be "in" SCOP already, i.e., no domains have been assigned so far (broadly, that's done by algorithms and a curator looking at their outputs). It is also not in CATH (SCOP's direct 'competitor') at this point. The curation efforts can't keep track with novel structures coming out, and more and more assignments will have to be made purely automatically (a development seen for sequences and their functions before). For SCOP, this transfer happens in SUPERFAMILY, it's sister resource. For CATH, that would be Gene3D. As a third option you can try the new Genome3D resource, which I think aims to be a bridge between the two (and some others things). A fourth option, which would be my personal favourite, is InterPro. It gives you a big picture (being a meta resource) and you can then "zoom in" by going to any of it's member databases (among which you'll find SUPERFAMILY and Gene3D, too). Importantly, in any of the mentioned resources, you would search by the UniProt ID (Q8K203) of your structure, which in this case I looked up in the PDB record for 3w0f. Results would be:
InterPro
http://www.ebi.ac.uk/interpro/protein/Q8K203
SUPERFAMILY
http://supfam.org/SUPERFAMILY/cgi-bin/gene.cgi?genome=up;seqid=Q8K203
Gene3D
http://gene3d.biochem.ucl.ac.uk/protein?smd5=c4942939b315f4c91a619918f1da713d
Genome3D
http://genome3d.eu/uniprot/id/Q8K203/annotations
After a while of using these resources you'll figure out their interconnections and redundancies, but - in some cases - also their individual benefits.
HTH,
Rob
It is neither classified in SCOPe, an automatic extension of the latest version of SCOP:
http://scop.berkeley.edu/pdb/code=3w0f
@Mary Ondrechen: it doesn't classify. i browsed the whole file. it's all like an error file. can you check?
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