Programatically accessing RCSB-PDB
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8.8 years ago
Bioaln ▴ 360

Hello. I've recently discovered RCSB already offers exactly what I need. SOme PDBs also have list of corresponding SNPs.(sequence/annotations/SNP). The problem is the following. I have way to many PDB accessions to manually download corresponding SNPs. Is there any way I could programatically access this site?

So to make things more clear, what I'm looking for is a way to in one script/program download for example

PDB: 4HHB AND its SNPs:

rs41486646 change: S-P
rs28928886 change: K-N
rs63749948 change: A-D
rs41497846 change: S-Y
rs63749791 change: L-V
rs41514946 change: S-R
rs41491146 change: F-L
rs33910377 change: P-LR 
..

I need just accession numbers (rs..). Can this be done?

Thank you for help

SNP pdb • 1.4k views
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Entering edit mode
8.8 years ago
Bioaln ▴ 360

I found something similar in the RCSB database dump!

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

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