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

摘要: In spite of the fact that many simplified model variants protein structure prediction have been widely studied in past years, few attention has given to discrete models with side chains, for which there is no specific benchmark. this paper, we propose an integer programming 3D-HP chain problem. The accounts energy resulting from all types interactions, between pairs backbone elements, hydrophilic chains and hydrophobic chains. Three sets instances, modified literature, were used experiments, maximum number non-local contact was found using ILOG CPLEX optimization package. We offer optimal solution several instances It expected mathematical allow further studies may, some cases, provide new values or bounds would rekindle interest fascinating problem domain.