I am trying to figure out how to search for an alpha helix or a b-strand followed by a sequence motif on the PDB. An example would be XFXXXAX -alpha helix. Does anybody know of a way to do this?
Thanks in advance. Paddy
Hi, you can get the sequences and secondary structure labels (by DSSP) of all PDB entries as a single big file from PDB website (https://cdn.rcsb.org/etl/kabschSander/ss.txt.gz). I'd iterate (e.g. with python) over all entries in this file looking for a sequence pattern of your choice which is followed by the alpha-helix. Alternatively, if you need more structural informations, you can get DSSP output for each entry from PDB (or clustered PDB to remove redundancy) which also have sequence and secondary structure information. Biopython has pretty nice parser for DSSP outputs which can help in tackling this programatically.
Good luck,
Janek
You may try with Robetta server: http://robetta.bakerlab.org/
you can get the sequences and secondary structure labels by using DSSP from PDB website (https://cdn.rcsb.org/etl/kabschSander/ss.txt.gz). or you can use PDBeMotif server (http://www.ebi.ac.uk/pdbe-site/pdbemotif/)
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