Towards a General Probabilistic Model of Protein Structure: The Reference Ratio Method

Abstract

The recently introduced reference ratio method[276] allows combining distributions over fine-grained variables with distributions over coarse-grained variables in a meaningful way. This problem is a major bottleneck in the prediction, simulation and design of protein structure and dynamics. Hamelryck et al. [276] introduced the reference ratio method in this context, and showed that the method provides a rigorous statistical explanation of the so called potentials of mean force(PMFs). These potentials are widely used in protein structure prediction and simulation, but their physical justification is highly disputed [32, 390, 715]. The reference ratio method clarifies, justifies and extends the scope of these potentials.