Structural Alignment and Trimming of Aligned Protein

[protein_fashion]

I have a protein domain that I am interested in, and I am looking at other proteins with the same domain, with the aim of performing electrostatic comparisons of them all. I have 750 similar domains, however in many cases they are part of a greater complex within pdb files.

What I am hoping to achieve, is structurally aligning my reference protein with a domain that is part of a larger complex (mobile), and then trim that larger structure based on the alignment, so that the output pdb file of the mobile structure is just the aligned domain. I have been trying to figure out a way to achieve this in Bio3D, but have yet to come up with a solution. I would imagine it could potentially be achieved using a combination of either struct.aln() or fit.xyz() and then trim.pdb() using output residue numbers from the alignment, but I have yet to figure it out. For instance, using chain A of pdb file 5D8E.pdb and then aligning it with 3KJO.pdb, and then trimming 3KJO.pdb to only output what was aligned with the 5D8E.pdb.

Thanks!

[Xinqiu Yao]

Make a pdbs object, fit all structures and output to a folder. Then, read fitted structures from the folder one by one and do the trimming. For example,

files <- list.files('.', '\\.pdb$') # this is original pdb files
pdbs <- pdbaln(files)
pdbfit(pdbs, outpath='fitlsq')

files2 <- list.files('fitlsq', full.names=TRUE)
pdbs2 <- pdbaln(files2)
# assume the first entry is the domain you want to find
inds <- !is.gap(pdbs2$ali[1, ])
for (i in pdbs2$id[-1]) {
   pdb <- read.pdb(i)
   resno <- pdbs2$resno[i, !is.gap(pdbs2$ali[i, ]) & inds]
   newpdb <- trim(pdb, resno=resno)
   write.pdb(newpdb, file=paste(i, '_trimed.pdb', sep=''))
}

Above just shows the idea but never tested. Let me know if you run into any troubles.

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