Table 2 Input features to the GNN architecture
From: Geometric deep learning improves generalizability of MHC-bound peptide predictions
Feature and shape and type | Description |
|---|---|
NODE FEATURES | |
res_type [21, 1], bool | One-hot representation of the node’s residue (20 amino acids + unknown). |
res_size [1], int | The number of non-hydrogen atoms in the side chain. |
res_mass [1], float | The average residue mass in Da. |
res_charge [1], int | The charge of the residue in fully protonated state in Coulomb. |
res_pI [1], float | The isoelectric point, i.e., the pH at which the molecule has no net electric charge. |
polarity [4, 1], bool | One-hot representation of the polarity of the amino acid: NONPOLAR, POLAR, NEGATIVE, POSITIVE. |
hb_donors [1], int | The number of hydrogen bond donor atoms in the residue. |
hb_acceptors [1], int | The number of hydrogen bond acceptor atoms in the residue. |
res_depth [1], float | The average distance in Å of the residue to the closest molecule of bulk water, computed via BioPython. |
hse [3, 1], float | Half sphere exposure, which indicates how buried an amino acid residue is in the biomolecule, computed via BioPython. |
sasa [1], float | Solvent-accessible surface area, in Å2, computed via FreeSASA. |
bsa [1], float | Buried surface area, which represents the area of the complex interface, in Å2, computed via FreeSASA. |
irc_total [1], int | The number of residues on the other chain that are within a cutoff distance of 5.5 Å. |
irc_negative_negative irc_negative_positive, irc_nonpolar_negative, irc_nonpolar_nonpolar, irc_nonpolar_polar, irc_nonpolar_positive, irc_polar_negative, irc_polar_polar, irc_polar_positive, irc_positive_positive [1], int | As above, but for specific residue polarity pairings. |
EDGE FEATURES | |
same_chain [1], bool | Boolean indicating whether the edge connects nodes belonging to the same chain (1) or separate chains (0). |
covalent [1], bool | Boolean indicating whether nodes are covalently bound (1) or not (0). Covalency is not directly assessed, but any edge with a maximum distance of 2.1 Å is considered covalent. |
electrostatic [1], float | Electrostatic potential (also known as Coulomb potential) between two nodes, calculated using interatomic distances and charges of each atom. |
vanderwaals [1], float | Van der Waals potential between two nodes, calculated using interatomic distances and a list of atoms with Van der Waals parameters. |
distance [1], float | Interatomic distance between atoms in Å, computed from the xyz atomic coordinates taken from the PDB file. |
