Computational energy-based redesign of robust proteins

The robustness of a system is a property that pervades all aspects of Nature. The ability of a system to adapt itself to perturbations due to internal and external agents, to aging, to wear, to environmental changes is one of the driving forces of evolution and a fundamental design principle. At the molecular level, understanding the robustness of a protein has a great impact on the in silicon design of polypeptide chains and drugs; the chance of computationally checking the ability of a protein to preserve its structure and function in the native state can lead to the design of new compounds that can work in a living cell more effectively. Inspired by the well known robustness analysis framework used in Electronic Design Automation, we introduced a notion of robustness for proteins and two dimensionless quantities: the energetic robustness and the energetic relative entropy. We used the energetic robustness in order to quantify the yield of a protein in terms of potential energy, an...

• Type: Journal
• Year: 2011
• Where: CCE
• Authors: Giovanni Stracquadanio, Giuseppe Nicosia
• Keywords: CCE 2011, Protein, Relative Entropy, Robustness, Software Engineering