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