RINs for small BioLiP enzymes (40-200 amino acids)

This dataset contains RINs for a set of single chain small enzymes (40-200 AAs) as well as a reference set of similar sized single chain non-enzymatic proteins. This work is related to the following paper: "Network analysis of residue interaction networks (RINs) for small single chain enzymes" by Michelle Ramsahoye and Mirela Alistar. The dataset structure is as follows: ref.zip (534 non-enzymatic proteins) Centralities - calculated centrality values using NetworkX on the RINs CIFs_cleaned - preprocessed CIFs, input for PDBe-Arpeggio JSONs - output from PDBe-Arpeggio PDBs_cleaned - preprocessed PDBs, input for PDBe-Arpeggio ref_enzyme_check_no_mc - sanity check to make sure no enzymes, no multichained proteins ref_set_raw - raw PDBs RINs - created residue interaction graphs SASA - using BioPython, SASA and RSA information test.zip (233 enzymatic proteins) biolip_lookup - Uses the BioLiP.txt file (available on BioLiP website here - https://zhanggroup.org/BioLiP/download.html) to determine functional residues for each protein chain Centralities - same as above except for this particular set of proteins CIFs_cleaned - same as above except for this particular set of proteins jackknife_experiment - output for each enzyme after running Jackknife procedure for each centrality value (MCC values, confusion matrices, thresholds, etc.) jackknife_explore_all_metrics - output for helping to determine what thresholds to use for the Jackknife procedure JSONs - same as above except for this particular set of proteins logs - logging from Arpeggio runs RIN_create_test - remnants of testing/sanity checking code RINs - same as above except for this particular set of proteins SASA - same as above except for this particular set of proteins ref_enzyme_check_no_mc - sanity check to make sure no multichained proteins test_set_raw - same as above except for this particular set of proteins