Predicting the receptor-binding domain usage of the coronavirus based on kmer frequency on spike protein

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Linear systems are characterized by two main properties: superposition and homogeneity. Superposition allows the response to multiple inputs to be the sum of the responses to each individual input. Homogeneity ensures that scaling an input by a scalar results in the response being scaled by the same scalar.
In contrast, nonlinear systems do not inherently possess these properties. However, for small deviations around an operating point, a nonlinear system can often be approximated as linear....

G-protein coupled receptors are ligand binding receptors that indirectly affect changes in the cell. The actual receptor is a single polypeptide that transverses the cell membrane seven times creating intracellular and extracellular loops. The extracellular loops create a ligand specific pocket which binds to neurotransmitters or hormones. The intracellular loops holds onto the G-protein.

Proportional-Derivative (PD) controllers are widely used in fan control systems to improve stability and performance. A fan control system can be effectively represented using a Bode plot to illustrate the impact of a PD controller through its transfer function. The Bode plot visually conveys how PD control modifies the fan's response across various frequencies, providing a frequency domain interpretation of the controller's behavior.
The proportional control gain, combined with the...

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Proportional-Integral (PI) controllers are essential in many control systems to improve stability and performance. They are commonly used in everyday devices like thermostats to enhance system damping and reduce steady-state error. When the zero in the controller's transfer function is optimally placed, the system benefits significantly in terms of stability and accuracy.
Acting as a low-pass filter, the PI controller slows the system's response and extends settling times. This requires...