Question: Pdb Structures Go Terms Clustering And Distance
1
gravatar for Reyhaneh
8.4 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

Hi;

I have two questions regarding Go terms;

1) I would clusters of PDB proteins using their Go Terms. Are there any available datasets for this?

2) Are there any metrics that can give a distance between proteins based on their Go terms? (similar to the distance we can get between two protein sequences pairs). I need this metric to say how much two proteins are different functionally. thanks in advance.

Reyhaneh

gene go • 2.4k views
ADD COMMENTlink modified 8.3 years ago by Rph10 • written 8.4 years ago by Reyhaneh480
3
gravatar for Khader Shameer
8.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

1) You can derive GO terms for your PDB structures using multiple approaches and use such terms for clustering

  • SCOP domain level annotation using SCOP2GO
  • Transfer of GO terms to individual protein chains using PDB Advanced Search interface
  • Use SIFTS annotations based on PDB chain to uniprot annotations (Use pdb_chain_go.lst)

2) If you have two GO terms you can compute semantic similarity (See this review for a background on basic concepts) between the terms. You can use packages like GoSemSim for such computations, extended list of tools here.

ADD COMMENTlink written 8.4 years ago by Khader Shameer18k
0
gravatar for Rph
8.4 years ago by
Rph10
Rph10 wrote:

Hi Reyhaneh,

You can download a file of GO annotations (gene association file) for PDB structures from the UniProt-GOA ftp site here; ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/

The file format is described in the associated readme.

I hope this helps.

Rachael.

ADD COMMENTlink written 8.4 years ago by Rph10
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