From Where Should I Get Data Set For Protein Structures?

Question

[Sagar Nikam]

i want protein structures data set for phylogeny comparison,whose PDB structures are present & protein seq length are similar (i.e.not differs much in length) with seq similarity at least 35%

if not possible,at least tell me PDB ids (35-100 are enough for me)

[Julien Textoris]

what about "please" "thanks" ...

Answer 1

[yatung]

Based on your description, I think you can simply download the protein sequences provided by RCSB PDB. Website: http://www.rcsb.org/pdb/download/download.do#otherDL Chooses the Download a FASTA file containing all PDB sequences. After the file is ready, you can do BLAST on all the protein sequences. The threshold of identities can define by yourself. Hope this helps!

[João Rodrigues]

Or just use the BLAST function within RCSB and define those options using the advanced query options.

Answer 2

[Ataly]

I am not sure to get your question. If you want to find a similar protein with a pdb file for a given sequence the ideal is to blast against the pdb: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins (withd atabase-->PDB)

[Sagar Nikam]

No sir i want diff protein structures but with comparable length to do alignment & then generate phylogenetic tree

Answer 3

[Tom Walsh]

Have a look at the Dunbrack lab's PISCES server for generating subsets of the PDB: http://dunbrack.fccc.edu/pisces/