Question: How to get PDB IDs for many fasta sequences?
0
gravatar for sl_99
9 days ago by
sl_990
sl_990 wrote:

Hello, there are 2600 untitled fasta sequences and I need to get PDB ID for each of them if it is possible. How can I do it without searching them in PDB manually, maybe using python script or something?

sequence python pdb • 104 views
ADD COMMENTlink modified 8 days ago by RamRS17k • written 9 days ago by sl_990
1

An alternative to blast would be HHPred too. This gives you PDB IDs as well as the relevant chains etc.

ADD REPLYlink written 9 days ago by jrj.healey6.8k

You could do blast searches at NCBI and use PDB database to search against. You could also do the search locally if you have blast+ installed.

ADD REPLYlink written 9 days ago by genomax55k
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