[Biopython] BLOCKS BLOSUM

[Eric Talevich]

HI George,

If the PDB ID isn't listed with the blocks, then I don't know of an
immediate way to look up the source structure PDBID, but since the blocks
are highly conserved (by definition) you should be able to get a reliable
hit by BLASTing with any of the sequences in the block against NCBI's PDBAA
database. If you'd like to be more rigorous you can construct an HMM profile
from the BLOCKS alignment and use HMMer to search PDBAA. And, if secondary
structure is all you're worried about, you can also try a secondary
structure prediction program like JPred with any of the source sequences as
the query.

Best,
Eric

On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> Hi,
> This might not be the correct place to ask this question-but some of you
> may
> have experience in this.
> I went to the BLOCKS database and downloaded a text file that contains many
> BLOCKS but I would like to see the structure of these blocks either in
> VMD/Pymol
> Is there a way to find the PDB ID of these blocks?
>
> What I want is to use the same BLOCKS info and develop my own BLOSUM like
> matrix using biopyhton.
> Thank you and my apologies is this is not directly related to biopython.
> (example of a block from the downloaded text file is given below)
> George
>
> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
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