Computational Design of a DNA- and Fc-Binding Fusion Protein

Figure 1

Chart of the design process. We employed a genetic algorithm (GA) with a fitness function based on secondary structure alignments and hydrophobicity and molecular weight comparisons. The resulting sequence set of this iterative process was refined using ERIS to build and rank the models which were then simulated using molecular dynamics simulations in order to estimate stability according to [4]. Amber and Brownian dynamics simulations are applied for testing and refinement of the final optimized protein models.