Peptide builder sample script
By Ivan Tubert-Brohman, upon a suggestion by Ramón Garduño-Vázquez
Builds a 3D structure for a peptide given a sequence (the structure is
essentialy linear; with some minor tweaks it could solve the protein-folding
problem ;-)
It uses mdl molfiles. I know that for peptides PDB would make more sense, but
for some reason I already had a few aminoacid structures in my drive as MDL
molfiles and was too lazy to deal with PDB. Some things would have to be
changed for it to generate a proper PDB file with the residue sequence numbers
and such.
# usage: ./pep.pl <SEQUENCE>
# prints an mdl molfile to stdout
# curent version only supports the residues A,G,L,V
FILES
peptide_builder.pl - the program
ala.mol - alanine with 3D coordinates
gly.mol - glycine with 3D coordinates
leu.mol - leucine with 3D coordinates
val.mol - valine with 3D coordinates
lava.mol - expected program output for ./peptide_builder LAVA