pb1729 / seq2pdbchain

go from amino acid sequence to unfolded chain in pdb format

Make PDB files for unfolded chains given an amino acid sequence

Start from an amino acid sequence and get a corresponding PDB file containing an unfolded protein with that sequence. The program makes an effort to avoid self-collisions and to generate a fairly compact chain. You can view the output and rerun if it is not satisfactory. Running an energy minimization afterwards is reccommended!

Usage:

Pick a destination file. eg. chains/8P59_unfolded.pdb. Then run the program:

python seq2pdbchain.py > chains/8P59_unfolded.pdb

the program will wait for you to paste in an amino acid sequence (use the standard single-letter code) eg:

GSHMVPISFVFNRFPRMVRDLAKKMNKEVNFIMRGEDTELDRTFVEEIGEPLLHLLRNAIDHGIEPKEERIAKGKPPIGTLILSARHEGNNVVIEVEDDGRGIDKEKIIRKAIEKGLIDESKAATLSDQEILNFLFVPGFSTKEKVSEVSGRGVGMDVVKNVVESLNGSISIESEKDKGTKVTIRLPLT

Now it will run. Progress will be printed to stderr while the actual PDB data will be written to stdout. Be warned, this can take a while. Longer sequences tend to take more time than short ones.

reached 20 residues
reached 40 residues
reached 60 residues
reached 80 residues
reached 100 residues
reached 120 residues
reached 140 residues
reached 160 residues
reached 180 residues
generated radii: 72.66125837695655,  82.63373094440966,  74.6990087257651,  93.86458597438353,  82.11500262414255,  117.79293476432316,  93.02286714315417,  104.19893614030393,  60.73629381203191,  53.44501330294728,  102.62828107208239,  91.5770164819002,  92.72031625730851,  68.278014329689,  131.72060255164962,  61.492131423541316
best: 53.445013