## 3 Feature Encoding Methods
### Physicochemical-Based Methods
It is an important concept in understanding the structure, function, and interactions of proteins and other biomolecules. The ASA can be calculated via various computational methods, with the most common approach being the rolling probe method. This method involves rolling a spherical probe (usually representing a water molecule) over the surface of the molecule and calculating the area that the probe can access without overlapping any atoms. The probe radius is typically set to 1.4 A, which is the approximate radius of a water molecule. Atomic radii: Each atom in a molecule is assigned a van der Waals radius. A spherical probe with a fixed radius (e.g., 1.4 A) is used to simulate the solvent. The surface area accessible to the probe is calculated by considering the overlap between the probe and the van der Waals surfaces of the atoms. **TA**  
Torsion angles, also known as dihedral angles, are crucial for describing the three-dimensional structure of proteins [136]. These angles define the spatial arrangement of atoms in the polypeptide backbone and side chains. The two most important torsion angles in proteins are the phi (\(\phi\)) and psi (\(\psi\)) angles, which describe the rotation around the bonds in the polypeptide backbone. Definitions: The phi angle is defined by the rotation around the bond between the nitrogen (N) and the alpha carbon (C\(\alpha\)) of an amino acid residue. It ranges from \(-180^{\circ}\) to \(+180^{\circ}\). The phi (\(\phi\)) angle affects the conformation of the backbone preceding the alpha carbon. The \(\psi\) angle is defined by the rotation around the bond between the alpha carbon (C\(\alpha\)) and the carbonyl carbon (C) of an amino acid residue. It also ranges from \(-180^{\circ}\) to \(+180^{\circ}\). The \(\psi\) angle affects the conformation of the backbone following the alpha carbon. The Ramachandran plot is a graphical representation of the allowed regions for the \(\phi\) and \(\psi\) angles in a protein structure. It helps visualise the steric constraints and preferred conformations of the polypeptide backbone. The plot is divided into regions corresponding to different secondary structures. The alpha helix typically has \(\phi\) and \(\psi\) angles of approximately (\(-57^{\circ}\), \(-47^{\circ}\)). Beta sheets typically have \(\phi\) and \(\psi\) angles of approximately (\(-139^{\circ}\), \(135^{\circ}\)) for parallel sheets and (\(-119^{\circ}\), \(113^{\circ}\)) for antiparallel sheets. A random coil covers a broader range of angles but avoids regions where steric clashes occur. Torsion angles can be calculated via the coordinates of the atoms in the polypeptide backbone. For a given residue i, the phi angle \(\phi\) i is defined by the atoms. **Z-Scale**  
The Z-scale is a method used in various fields to standardise data [137]. It is particularly known for its application in protein structure analysis and machine learning. In the context of protein structure analysis, the Z-scale is a set of numerical indices that describe the physicochemical properties of amino acids. These indices are derived from experimental data and are used to predict protein structure and function. The Z-scale is used to describe the properties of amino acids in a protein sequence. These properties can help predict the secondary and tertiary structures of proteins by providing insights into how amino acids interact with each other.