Features

Prop3D calculates the features for every atom in every protein/domain in a dataset, saving all results into different HDF datasets for each protein.

For atom-level features, we create one-hot encodings for 23 AutoDock atom names, 16 element names, and 21 residue types (20 standard amino acids and one UNKnown placeholder). We also include van der Waals radii, charges from Pdb2Pqr (Q62856803), electrostatic potentials computed via APBS (Q65072984), concavity values that we calculate via CX (Q114841750), various hydrophobicity features of the residue that an atom belongs to (Kyte-Doolite, Biological and Octanol), and two measures of accessible surface area (per-atom, via FreeSASA (Q114841793), and per-residue via DSSP (Q5206192)). We also include different types of secondary structure information: one-hot encodings for DSSP (Q5206192)) 3- and 7- secondary structure classifications, as well as the backbone torsion angles ($phi$, $psi$; along with embedded sine and cosine transformations of each). We also annotate aromaticity, and hydrogen bond acceptors and donors, based on AutoDock atom-name types. As a gauge of phylogenetic conservation, we include sequence entropy scores from EPPIC (Q114841783). These biophysical, physicochemical, structural, and phylogenetic features are summarized above and are exhaustively enumerated in the tables below.

We also provide functionality to create discretized values of features via the application of Boolean logic operators to the corresponding continuous-valued quantities of a given descriptor, using simple numerical thresholding (Table ref{table:bool-feats}).

All Features

Source Features (1-hot and continuous values)

Feature	Voxel Aggregation Rule	Residue Aggregation Rule	Source Software or Database
H	max		MGLTools (Q114840701)
HD	max		MGLTools (Q114840701)
HS	max		MGLTools (Q114840701)
C	max		MGLTools (Q114840701)
A	max		MGLTools (Q114840701)
N	max		MGLTools (Q114840701)
NA	max		MGLTools (Q114840701)
NS	max		MGLTools (Q114840701)
OA	max		MGLTools (Q114840701)
OS	max		MGLTools (Q114840701)
F	max		MGLTools (Q114840701)
MG	max		MGLTools (Q114840701)
P	max		MGLTools (Q114840701)
SA	max		MGLTools (Q114840701)
S	max		MGLTools (Q114840701)
CL	max		MGLTools (Q114840701)
CA	max		MGLTools (Q114840701)
MN	max		MGLTools (Q114840701)
FE	max		MGLTools (Q114840701)
ZN	max		MGLTools (Q114840701)
BR	max		MGLTools (Q114840701)
I	max		MGLTools (Q114840701)
Unk_atom	max		MGLTools (Q114840701)
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	yes	cite{Bondi1964}
partial charge (charge)	mean	sum	Pdb2Pqr (Q62856803)
electrostatic_potential	mean	sum	APBS (Q65072984)
concavity (cx)	mean	mean	CX (Q114841750)
hydrophobicity	mean	yes	Kyte-Doolittle
biological_hydrophobicity	mean	yes	cite{Hessa2005}
octanal_hydrophobicity	mean	yes	Wimley-White 1996
atom_asa	mean		FreeSASA (Q114841793)
residue_rasa	mean	yes	DSSP (Q5206192)
ALA	max	yes	PDB File
CYS	max	yes	PDB File
ASP	max	yes	PDB File
GLU	max	yes	PDB File
PHE	max	yes	PDB File
GLY	max	yes	PDB File
HIS	max	yes	PDB File
ILE	max	yes	PDB File
LYS	max	yes	PDB File
LEU	max	yes	PDB File
MET	max	yes	PDB File
ASN	max	yes	PDB File
PRO	max	yes	PDB File
GLN	max	yes	PDB File
ARG	max	yes	PDB File
SER	max	yes	PDB File
THR	max	yes	PDB File
VAL	max	yes	PDB File
TRP	max	yes	PDB File
TYR	max	yes	PDB File
Unk_residue	max	yes	PDB File
phi	mean	yes	BioPython (Q4118434)
phi_sin	mean	yes	NumPy
phi_cos	mean	yes	NumPy
psi	mean	yes	BioPython (Q4118434)
psi_sin	mean	yes	NumPy
psi_cos	mean	yes	NumPy
is_helix	max	yes	DSSP (Q5206192)
is_sheet	max	yes	DSSP (Q5206192)
Unk_SS	max	yes	DSSP (Q5206192)
is_regular_helix	max	yes	DSSP (Q5206192)
is_beta_bridge	max	yes	DSSP (Q5206192)
is_extended_strand	max	yes	DSSP (Q5206192)
is_310_helix	max	yes	DSSP (Q5206192)
is_pi_helix	max	yes	DSSP (Q5206192)
is_hbond_turn	max	yes	DSSP (Q5206192)
is_bend	max	yes	DSSP (Q5206192)
no_ss	max	yes	DSSP (Q5206192)
hydrophobic_atom	max		MGLTools (Q114840701)
aromatic_atom	max		MGLTools (Q114840701)
hbond_acceptor	max		MGLTools (Q114840701)
hbond_donor	max		MGLTools (Q114840701)
metal	max		MGLTools (Q114840701)
eppic_entropy	min	yes	EPPIC (Q114841783)

Boolean Features (Derived from Above Features)

Boolean Feature	Source Feature	Equality	Threshold
neg_charge	charge	<	0
pos_charge	charge	>	0
is_electronegative	electrostatic_potential	<	0
is_concave	cx	leq	2
is_hydrophobic	hydrophobicity	>	0
residue_buried	residue_rasa	<$	0.2
is_conserved	eppic_entropy	<	0.5

Feature Subsets

Many of the features are no doubt correlated, so you should pick a small subset of features that are of interest. We have created a few subsets of data that can be used to train model or use as labels.

standard

‘C’, ‘A’, ‘N’, ‘OA’, ‘OS’, ‘C_elem’, ‘N_elem’, ‘O_elem’, ‘S_elem’, ‘is_helix’, ‘is_sheet’, ‘residue_buried’, ‘is_hydrophobic’, ‘pos_charge’, ‘is_electronegative’

get_atom_type

‘H’, ‘HD’, ‘HS’, ‘C’, ‘A’, ‘N’, ‘NA’, ‘NS’, ‘OA’, ‘OS’, ‘F’, ‘MG’, ‘P’, ‘SA’, ‘S’, ‘CL’, ‘CA’, ‘MN’, ‘FE’, ‘ZN’, ‘BR’, ‘I’, ‘Unk_atom’

get_element_type

‘C_elem’, ‘N_elem’, ‘O_elem’, ‘S_elem’, ‘H_elem’, ‘F_elem’, ‘MG_elem’, ‘P_elem’, ‘CL_elem’, ‘CA_elem’, ‘MN_elem’, ‘FE_elem’, ‘ZN_elem’, ‘BR_elem’, ‘I_elem’, ‘Unk_elem’

get_charge_and_electrostatics

‘charge’, ‘neg_charge’, ‘pos_charge’, ‘electrostatic_potential’, ‘is_electronegative’

get_concavity

‘cx’, ‘is_concave’

get_hydrophobicity

‘hydrophobicity’, ‘is_hydrophobic’, ‘biological_hydrophobicity’, ‘octanal_hydrophobicity’

get_accessible_surface_area

‘atom_asa’, ‘residue_rasa’, ‘residue_buried’

get_residue

‘ALA’, ‘CYS’, ‘ASP’, ‘GLU’, ‘PHE’, ‘GLY’, ‘HIS’, ‘ILE’, ‘LYS’, ‘LEU’, ‘MET’, ‘ASN’, ‘PRO’, ‘GLN’, ‘ARG’, ‘SER’, ‘THR’, ‘VAL’, ‘TRP’, ‘TYR’, ‘Unk_residue’

get_ss

‘phi’, ‘phi_sin’, ‘phi_cos’, ‘psi’, ‘psi_sin’, ‘psi_cos’, ‘is_helix’, ‘is_sheet’, ‘Unk_SS’, ‘is_regular_helix’, ‘is_beta_bridge’, ‘is_extended_strand’, ‘is_310_helix’, ‘is_pi_helix’, ‘is_hbond_turn’, ‘is_bend’, ‘no_ss’

get_deepsite_features

‘hydrophobic_atom’, ‘aromatic_atom’, ‘hbond_acceptor’, ‘hbond_donor’, ‘metal’

get_evolutionary_conservation_score

‘eppic_entropy’, ‘is_conserved’

get_frustration

‘density_res’, ‘native_energy’, ‘decoy_energy’, ‘sd_energy’, ‘frustration_index’, ‘is_highly_frustrated’, ‘is_minimally_frustrated’, ‘has_neutral_frustration’