Fully computational design of SaCas9 with relaxed PAM requirement

Data Structure This repository contains the UniDesign program, scripts, and result summary for SaCas9 PAM relaxation from NNGRRT to NNNRRT. UniDesign.tar.gz This compressed archive contains the UniDesign package. Users may need to recompile the UniDesign executable located in the UniDesign directory. data_files.zip This compressed archive contains dna_mut_file.txt, which is used to build DNA mutant models, as well as the UniDesign RESFILEs used across three design iterations. pdbs.zip This compressed archive contains input PDB structural models with diOerent PAM sequences (g3a: TTAGGT, g3c: TTCGGT, g3g: TTGGGT, and g3t: TTTGGT). scripts.zip This compressed archive contains Perl and Python scripts used for PAM-relaxation design and analysis. mutant_summary.zip This compressed archive contains summary_*.tsv files generated by the Python script, which are renamed as DataS*.xlsx. list_5axw1_pam_relax_g3n This file contains a list of PDB structural models saved in pdbs.zip. unidesign_models.tar.bz2 This compressed archive contains all UniDesign-generated data, including the structural models and energetic data. UniDesign Job Submission UniDesign jobs are submitted using scripts/submit_pam_relax_design.pl. Usage: ./scripts/submit_pam_relax_design.pl <pdb1> <pam> <step> <min_mut> <max_mut> <n_designs> <run> Example: ./scripts/submit_pam_relax_design.pl 5axw1 g3n step1 0 1 1000 run1 The designs will be saved into the designs_pam_relax_{pam}_{run}/{pdb1}_{g3[a,c,g,t]}_{step}_{min_mut}_{max_mut}. For example, in the first design iteration, we have {pam} = “g3n”; {run} = “run1”, “run2”, …, “run10”; {pdb1} = “5axw1”; {g3[a,c,g,t]} = “g3a”, “g3c”, “g3g”, or “g3t”; {step} = “step1”; {min_mut} = 0, {max_mut} = 1. In the second and third iterations, we have {step} = “step2” and “step3”, respectively. Energetic analysis of UniDesign designs The UD_designs.tsv under designs_pam_relax_{pam}_{run}/{pdb1}_{g3[a,c,g,t]}_{step}_{min_mut}_{max_mut} (see unidesign_models.tar.bz2) will be analyzed by scripts/run_analyze_comm_mutants2.py. Usage: ./scripts/run_analyze_comm_mutants2.py <pdb1> <pam> <list_pdbs> <stepn> <min_muts> <max_muts> Example: ./scripts/run_analyze_comm_mutants2.py 5axw1 g3n list_5axw1_pam_relax_g3n step1 0 1 > summary_5axw1_pam_relax_g3n_step1_0_1.tsv Running the above command will redirect the result into summary_5axw1_pam_relax_g3n_step1_0_1.tsv (see mutant_summary folder).