Reducing the computational load of energy evaluations for protein folding

Predicting the native conformation using computational protein models requires a large number of energy evaluations even with simplified models such as hydrophobic-hydrophilic (HP) models. Clearly, energy evaluations constitute a significant portion of computational time. We hypothesize that given the structured nature of algorithms that search for candidate conformations such as stochastic methods, energy evaluation computations can be cached and reused, thus saving computational time and effort. In this paper, we present a caching approach and apply it to the triangular 2D-HP lattice model. We provide theoretical analysis and prediction of the expected savings from caching as applied this model. We conduct experiments using a sophisticated evolutionary algorithm that contains elements of local search, memetic algorithms, diversity replacement, etc. in order to verify our hypothesis and demonstrate a significant level of savings in computational effort and time that caching can provide.