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'HY': 'red', # Hydrophobic
'HB': 'blue', # Hydrogen Bond
'AT': 'green', # Attractive
'RE': 'orange', # Repulsive
'SB': 'pink', # Salt Bridge
'DS': 'purple' # Disulfide Bond
COCαDA (Contact Optimization by alpha-Carbon Distance Analysis) optimizes the calculation of atomic interactions in proteins, by using a set of fine-tuned Cα distances between every pair of aminoacid residues. The code includes a customized parser for both PDB and CIF files, containing functionalities for handling large files, filtering out specific residues and interactions, and calculating geometric properties such as centroid and normal vectors for aromatic residues.
LEMOS, Rafael P.; MARIANO, Diego; SILVEIRA, Sabrina A.; MELO-MINARDI, Raquel C. de. COCαDA - Large-Scale Protein Interatomic Contact Cutoff Optimization by Cα Distance Matrices. In: Proceedings of the XVII Brazilian Symposium on Bioinformatics (BSB), 17, p. 59-70, 2024. DOI: https://doi.org/10.5753/bsb.2024.245545
