A simple way to compute protein dynamics without a mechanical model

Abstract

We found that in proteins the average atomic fluctuation is linearly related to the square of the atomic distance from the center of mass of the protein. Using this simple relation, we can accurately compute the temperature factors of proteins of a wide range of sizes and folds, and the correlation of the fluctuations in proteins. This simple relation provides a direct link between protein dynamics and the static protein's geometrical shape and offers a simple way to compute protein dynamics without either long time trajectory integration or any matrix operations.