One way of visualizing what a protein looks like
Molecular mechanics (MM) is the mathematical representation of atomic interactions. MM was developed and applied over 50 years ago for organic chemistry as a tool to estimate specific energetic properties of small molecules. Since then it has evolved into various functional forms (known as “force fields”) used to describe the potential energy of a system by computing atomic interactions. Force fields may vary in the way that they represent atomic particles to balance experimental accuracy with computational efficiency. Molecular dynamics (MD) is a MM-based method in which force fields are used to calculate the positions and velocities of atoms over time to produce a trajectory.
