corydupai / Beta-hairpins

Code to identify/analyze beta hairpin motifs in pdb files

Beta hairpins

Code to identify/analyze beta hairpin motifs in pdb files

Key scripts

• scripts/parse_secondary_structures.R finds motifs in pdb files
• main.Rmd does most of the heavy lifting on analysis and figure generation
• logo_generation.Rmd makes the motiff logo for supplemental figure
• make_dssp.sh converts pdb .cif.gz files to .dssp like files with secondary structure info but no headers

Data files

• data/beta_hairpin_pairs.csv has info on contacting residues between beta strands of analyzed sequences
• data/beta_hairpin_sequences.csv has info on included sequences
• data_mid/pair_data_bigger.csv.gz has all of the pairs output by scripts/parse_secondary_structures.R. Unzip this to read into main.Rmd