An integer programming model for protein structure prediction using the 3D-HP side chain model (Q897607)

In this paper the authors focus on discrete models with side chains and propose an integer programming approach for the 3D-HP side chain protein structure problem. Following an introduction of the prediction problem and an overview of discrete and continuous models proposed for the analysis of the folding process, the authors present in detail the 3D-HP-SC integer programming formulation. First, the mathematical notation is introduced. Next, the accepted interactions between backbones and hydrophilic and hydrophobic side chains are presented. In the next sections, the variables and formulations are described in detail. The paper concludes with an overview of the computational experiments conducted on the ILOG CPLEX optimisation package (details on runtimes and resources are also included). For several instances, previously described in the literature, the optimal solution is reached, using this programming approach.