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software used in paper "Antibody interface prediction with 3D Zernike descriptors and SVM"
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README.md

AntibodyInterfacePrediction

software used in paper "Antibody interface prediction with 3D Zernike descriptors and SVM"

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The "test" binary (Linux x64) can be used to generate the testing samples from an Ab-Ag pair. Two PDB files must be provided at runtime in the command line.

Paratope prediction - Test samples generator. Usage: -h [ --help ] Display this brief help message.

--receptor arg Name of the Antibody's PDB file.

--ligand arg Name of the Antigen's PDB file.

--atom_radii arg File containing the radius information of each atom. If not specified, the default CHARMM22 radius values will be used for PDB files. It is ignored if specified for PQR files.

--no_hetatm Ignore HETATM records in the surface computation.

--no_hydrogen Ignore hydrogen atoms in the surface computation. NOTE: X-ray crystallography cannot resolve hydrogen atoms in most protein crystals, so in most PDB files, hydrogen atoms are absent. Sometimes hydrogens are added by modeling. Hydrogens are always present in PDB files resulting from NMR analysis, and are usually present in theoretical models.

-p [ --probe_radius ] arg (=1.4) Probe radius (in Å), floating point number in (0, 2.0] (default is 1.4Å).

-R [ --patch_radius ] arg (=6) Patch radius (in Å), positive floating point (default is 6.0Å).

-i [ --interface_distance ] arg (=4.5) Threshold distance for the interface determination (in Å), positive floating point (default is 6.0Å).

-d [ --patch_dist ] arg (=1.8) Minimum distance between patch centers (in Å), positive floating point (default is 1.8Å).

-r [ --resolution ] arg (=4) Resolution factor, positive floating point (default is 4.0). This value's cube determines the number of voxels per ų.

-N [ --max_order ] arg (=5) Maximum Zernike descriptor order (default is 5).

-l [ --license ] View license information.

-v [ --version ] Display the version number

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The "train" binary (Linux x64) can be used to generate the training samples from an Ab-Ag pair. Two PDB files must be provided at runtime in the command line.

Paratope prediction - Training samples generator. Usage: -h [ --help ] Display this brief help message.

--receptor arg Name of the Antibody's PDB file.

--ligand arg Name of the Antigen's PDB file.

--atom_radii arg File containing the radius information of each atom. If not specified, the default CHARMM22 radius values will be used for PDB files. It is ignored if specified for PQR files.

--no_hetatm Ignore HETATM records in the surface computation.

--no_hydrogen Ignore hydrogen atoms in the surface computation. NOTE: X-ray crystallography cannot resolve hydrogen atoms in most protein crystals, so in most PDB files, hydrogen atoms are absent. Sometimes hydrogens are added by modeling. Hydrogens are always present in PDB files resulting from NMR analysis, and are usually present in theoretical models.

-p [ --probe_radius ] arg (=1.4) Probe radius (in Å), floating point number in (0, 2.0] (default is 1.4Å).

-R [ --patch_radius ] arg (=6) Patch radius (in Å), positive floating point (default is 6.0Å).

-i [ --interface_distance ] arg (=4.5) Threshold distance for the interface determination (in Å), positive floating point (default is 6.0Å).

--patch_dist_i arg (=1) Minimum distance between interface patch centers (in Å), positive floating point (default is 1.0Å).

--patch_dist_n arg (=3) Minimum distance between non-interface patch centers (in Å), positive floating point (default is 3Å).

-r [ --resolution ] arg (=4) Resolution factor, positive floating point (default is 4.0). This value's cube determines the number of voxels per ų.

-N [ --max_order ] arg (=5) Maximum Zernike descriptor order (default is 5).

-l [ --license ] View license information.

-v [ --version ] Display the version number

########################################################################

The "single_structure_descriptors" binary (Linux x64) can be used to generate the classification samples from a Ab structure. The Ab's PDB file must be provided at runtime in the command line.

Paratope prediction - Classification samples generator. Usage: -h [ --help ] Display this brief help message.

--input_pdb arg Name of the Antibody's PDB file.

--atom_radii arg File containing the radius information of each atom. If not specified, the default CHARMM22 radius values will be used for PDB files. It is ignored if specified for PQR files.

--no_hetatm Ignore HETATM records in the surface computation.

--no_hydrogen Ignore hydrogen atoms in the surface computation. NOTE: X-ray crystallography cannot resolve hydrogen atoms in most protein crystals, so in most PDB files, hydrogen atoms are absent. Sometimes hydrogens are added by modeling. Hydrogens are always present in PDB files resulting from NMR analysis, and are usually present in theoretical models.

-p [ --probe_radius ] arg (=1.4) Probe radius (in Å), floating point number in (0, 2.0] (default is 1.4Å).

-R [ --patch_radius ] arg (=6) Patch radius (in Å), positive floating point (default is 6.0Å).

-d [ --patch_dist ] arg (=1.8) Minimum distance between patch centers (in Å), positive floating point (default is 1.8Å).

-r [ --resolution ] arg (=4) Resolution factor, positive floating point (default is 4.0). This value's cube determines the number of voxels per ų.

-N [ --max_order ] arg (=5) Maximum Zernike descriptor order (default is 5).

-l [ --license ] View license information.

-v [ --version ] Display the version number

########################################################################

The "CHARMM22" file contains the atomic radii information used during the surface computation process. Users can append new entries at the end of this file, modify existing ones, or create their own file with the desired radius assignment for each atom type. It is required by both the "train" and "test" binaries to function correctly. The easiest way to correctly run the binaries would be to place all files in the same directory: train/test binary, CHARMM22 file and the two PDB files. The location of the CHARMM22 file can also be supplied to the binaries with the "--atom_radii" command line option followed with the full path to the file.

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