protein-DNA complex pdbaln() possible?

[Former user]

Would it be possible in Bio3d to do blast search for protein-DNA complex (e.g. 1BPX) using protein sequence but then fetch entire PDBs and align them using pdbaln () (only protein coordinates) and finally superimpose entire PDB including DNA coordinates?

I am interested in seeing the structural changes of the DNA coordinates in the final superimposition and just not protein.

[Lars Skjærven]

absolutely. this could be a start:

seq = get.seq("1BPX_A")
blast = blast.pdb(seq)
hits = plot.blast(blast)

# fetch 5 of the PDBs
raw.files <- get.pdb(hits$pdb.id[1:5], path = "raw_pdbs", gzip=TRUE)

# align structures
pdbs <- pdbaln(raw.files)

# find invariant core
core <- core.find(pdbs)

# superimpose all structures to core
pdbs$xyz = pdbfit(pdbs, core$c0.5A.xyz, outpath="fitlsq")

[Lars Skjærven]

reopen if needed