Protein sequence optimization

Many structural bioinformatics approaches employ sequence profile-based threading algorithms. To improve fold recognition rates, homology searching may include artificially evolved amino acid sequences. We developed eVolver, an optimization engine that evolves protein sequences to stabilize the respective structures by a variety of potentials. Sequences generated by eVolver have high capabilities to recognize the correct protein structures using standard sequence profile-based techniques, thus they can be incorporated into existing threading approaches to increase their sensitivity. These sequences also provide a linkage between protein structure and function in computer simulations focused on the study of the completeness of protein structure space.