thanks very much for your shared codes and paper!!
I use RF diffusion to generate, ProteinMPNN-FastRelax, and finally af2_initial_guess, all the default configs.
I test short peptide length 6-10 amino acids, and longer length 26-30 amino acids for the 2 different target proteins.
After run 1000 designs and all the same phenomena:
In the new pdb which is generate from af2 prediction, the distance between binder and target becomes much longer.
In the pictures blew, the green color is the pdb after ProteinMPNN-FastRelax; the cyan color is the pdb after af2_initial_guess prediction.
Questions:
is this noraml or designed on purpose?
in my case, all the pae_interaction are between 22-28, too larger, that's low quality. When the designed structured from ProteinMPNN-FastRelax is low quality, the distance between binder and target becomes much longer?
Maybe some target protein structures are very hard to design good bindiers.
could you supply a target pdb and binder design configs to let me have a pae_interaction < 10 for 1000 designs?
thanks very much in advace!!
thanks for your innovation on af2_initial_guess, a really good idea!!
pdbs.zip
Hi @nrbennet
thanks very much for your shared codes and paper!! I use RF diffusion to generate, ProteinMPNN-FastRelax, and finally af2_initial_guess, all the default configs. I test short peptide length 6-10 amino acids, and longer length 26-30 amino acids for the 2 different target proteins.
After run 1000 designs and all the same phenomena: In the new pdb which is generate from af2 prediction, the distance between binder and target becomes much longer. In the pictures blew, the green color is the pdb after ProteinMPNN-FastRelax; the cyan color is the pdb after af2_initial_guess prediction.
Questions: