Table 3 All protein descriptors and extracted features that are defined and calculated in Prop3D
Feature | Voxel aggregation rule | Residue aggregation rule | Source software or database | Wikidata entry |
|---|---|---|---|---|
H | max | MGLTools | ||
HD | max | MGLTools | ||
HS | max | MGLTools | ||
C | max | MGLTools | ||
A | max | MGLTools | ||
N | max | MGLTools | ||
NA | max | MGLTools | ||
NS | max | MGLTools | ||
OA | max | MGLTools | ||
OS | max | MGLTools | ||
F | max | MGLTools | ||
MG | max | MGLTools | ||
P | max | MGLTools | ||
SA | max | MGLTools | ||
S | max | MGLTools | ||
CL | max | MGLTools | ||
CA | max | MGLTools | ||
MN | max | MGLTools | ||
FE | max | MGLTools | ||
ZN | max | MGLTools | ||
BR | max | MGLTools | ||
I | max | MGLTools | ||
Unk_atom | max | MGLTools | ||
C_elem | max | PDB File | ||
N_elem | max | PDB File | ||
O_elem | max | PDB File | ||
S_elem | max | PDB File | ||
H_elem | max | PDB File | ||
F_elem | max | PDB File | ||
MG_elem | max | PDB File | ||
P_elem | max | PDB File | ||
CL_elem | max | PDB File | ||
CA_elem | max | PDB File | ||
MN_elem | max | PDB File | ||
FE_elem | max | PDB File | ||
ZN_elem | max | PDB File | ||
BR_elem | max | PDB file | ||
I_elem | max | PDB file | ||
Unk_elem | max | PDB file | ||
vdw | mean | \(\checkmark\) | [62] | |
Partial charge (charge) | Mean | sum | Pdb2Pqr | |
electrostatic_potential | mean | sum | APBS | |
concavity (cx) | mean | mean | CX | |
hydrophobicity | mean | \(\checkmark\) | Kyte-Doolittle [39] | |
biological_hydrophobicity | mean | \(\checkmark\) | [40] | |
octanal_hydrophobicity | mean | \(\checkmark\) | Wimley-White [41] | |
atom_asa | mean | FreeSASA | ||
residue_rasa | mean | \(\checkmark\) | DSSP | |
ALA | max | \(\checkmark\) | PDB file | |
CYS | max | \(\checkmark\) | PDB file | |
ASP | max | \(\checkmark\) | PDB file | |
GLU | max | \(\checkmark\) | PDB file | |
PHE | max | \(\checkmark\) | PDB file | |
GLY | max | \(\checkmark\) | PDB file | |
HIS | max | \(\checkmark\) | PDB file | |
ILE | max | \(\checkmark\) | PDB file | |
LYS | max | \(\checkmark\) | PDB file | |
LEU | max | \(\checkmark\) | PDB file | |
MET | max | \(\checkmark\) | PDB file | |
ASN | max | \(\checkmark\) | PDB file | |
PRO | max | \(\checkmark\) | PDB file | |
GLN | max | \(\checkmark\) | PDB file | |
ARG | max | \(\checkmark\) | PDB file | |
SER | max | \(\checkmark\) | PDB file | |
THR | max | \(\checkmark\) | PDB file | |
VAL | max | \(\checkmark\) | PDB file | |
TRP | max | \(\checkmark\) | PDB file | |
TYR | max | \(\checkmark\) | PDB file | |
Unk_residue | max | \(\checkmark\) | PDB file | |
phi | mean | \(\checkmark\) | BioPython | |
phi_sin | mean | \(\checkmark\) | NumPy | |
phi_cos | mean | \(\checkmark\) | NumPy | |
psi | mean | \(\checkmark\) | BioPython | |
psi_sin | mean | \(\checkmark\) | NumPy | |
psi_cos | mean | \(\checkmark\) | NumPy | |
is_helix | max | \(\checkmark\) | DSSP | |
is_sheet | max | \(\checkmark\) | DSSP | |
Unk_SS | max | \(\checkmark\) | DSSP | |
is_regular_helix | max | \(\checkmark\) | DSSP | |
is_beta_bridge | max | \(\checkmark\) | DSSP | |
is_extended_strand | max | \(\checkmark\) | DSSP | |
is_310_helix | max | \(\checkmark\) | DSSP | |
is_pi_helix | max | \(\checkmark\) | DSSP | |
is_hbond_turn | max | \(\checkmark\) | DSSP | |
is_bend | max | \(\checkmark\) | DSSP | |
no_ss | max | \(\checkmark\) | DSSP | |
hydrophobic_atom | max | MGLTools | ||
aromatic_atom | max | MGLTools | ||
hbond_acceptor | max | MGLTools | ||
hbond_donor | max | MGLTools | ||
metal | max | MGLTools | ||
eppic_entropy | min | \(\checkmark\) | EPPIC |