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...

Sigmatropic rearrangements are a class of pericyclic reactions in which a σ bond migrates from one part of a π system to another. These are intramolecular rearrangements where the total number of σ and π bonds remain unchanged.
Sigmatropic shifts are classified based on an order term [i, j ], where i and j indicate the number of atoms across which each end of the σ bond migrates. Below are examples of a [3,3] sigmatropic shift in...

State-space representation is a powerful tool for simulating physical systems on digital computers, necessitating the conversion of the transfer function into state-space form. Consider an nth-order linear differential equation with constant coefficients, like those encountered in an RLC circuit. The state variables are selected as the output and its n−1 derivatives. Differentiating these variables and substituting them back into the original equation produces the state equations.
In an...