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