Hello,
I am using Pepspec to optimize a 10mers peptide sequence to better binding to a membrane protein. In the design, I kept the first residue constant, while mutating the rest by all 20 amino acids. The flags file is the following:
-in:file:s ppk_complex_0001.pdb
-pepspec::pep_chain B
-pepspec::pep_anchor 1
-pepspec::n_append 9
-pepspec::n_peptides 10000
-ignore_unrecognized_res
-ex1
-ex2
-extrachi_cutoff 0
-score::weights ref2015.wts
-pepspec::soft_wts soft_rep.wts
-pepspec::interface_cutoff
-pepspec::clash_cutoff 5.0
-pepspec::n_build_loop 100
-pepspec::diversify_pep_seqs
-pepspec::diversify_lvl 10
-pepspec:remove_input_bb
-pepspec:gen_pep_bb_sequential
-pepspec::save_low_pdbs
-o pepspec_complex
-out:file:design_contrast redesign_complex
-out:file:silent pepspec_complex_redesign.silent
-out:file:silent_struct_type binary
-out:file:fullatom
-out:file:scorefile pepspec_complex_redesign
The run generated 990668 non-redundant sequences and saved 10000 pdbs. Then I used WebLogo to evaluate the quality of the sampling (see attached picture). As can be seen, there is an over-enrichment of Ser and Gly along the sequence, which looks weird to me. Is this an artifact of the sampling? How can I improve the sampling?
Thanks in advance,
Yasser
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