This package contains all computational data for the work titled "Decoding CRISPR–Cas9 PAM recognition with UniDesign" by Huang et al.

00_Cas9s-preprocessed-PDBs.tar.bz2 : 10 preprocessed PDBs.

01_perl-scripts.tar.bz2: all perl scripts used in this study. This UniDesign software is not included in this package.

02_PAM-variants-PDBs.tar.bz2: all PAM variant combos for each of the ten PDB scaffolds.

02_list-Cas9s-PAM-variants.tar.bz2: lists of all PAM variant combos for each of the ten PDB scaffolds.

03_PAM-recognition-Cas9s.tar.bz2: all PIAA-repacked structure models and energy scores.

03_PAM-recognition-top-bind-and_total_energy.tar.bz2 : summary of all UniDesign-calculated binding and total energy scores for each 
PAM variant of each Cas9. The PAM-recognition-*.txt files were generated using Perl script run_collect_PAM_recognition_seqs.pl. 
The PAM-recognition-*.txt.sort files were generated using run_sort_by_bind_and_tot_energy.pl. The PAM-recognition-*.txt.sort.*-*.txt 
files were generated using Perl script run_select_low_energy.pl. The preferred PAM variants can be extracted from the first field of 
the PAM-recognition-*.txt.sort.*-*.txt files.

03_RESFILE-PAM-recognition.tar.bz2: all RESFILEs for computational PAM recognition experiments.

04_PIAA-design-Cas9s-PDB-PAMs.tar.bz2: all PIAA-redesigned structure models and energy scores using PDB PAMs.

05_models-consensus-PAM-Cas9s.tar.bz2: all Cas9 structure models bearing consensus PAMs.

05_list-Cas9s-PIAA-design-consensus-PAMs.tar.bz2: lists of all Cas9 structure models bearing consensus PAMs.

06_PIAA-design-Cas9s-consensus-PAMs.tar.bz2: all PIAA-redesigned structure models and energy scores. The redesigned PIAAs 
can be extracted from *bestseqs.txt, *bestsites0001.pdb and/or *beststruct0001.pdb files.

06_RESFILE-PIAA-design.tar.bz2: all RESFILEs for computational PIAA redesign experiments.