Protein engineering in the computational age: An open source framework for exploring mutational landscapes in silico

Area of Science:

• Synthetic Biology
• Protein Engineering
• Computational Biology

Background:

• Protein engineering has expanded significantly, driven by computational tools and high-throughput screening.
• Expertise in computational biology and structural biochemistry is often a bottleneck for complex protein engineering projects.
• The International Genetically Engineered Machine (iGEM) competition offers a platform for synthetic biology innovation but faces challenges with complex projects.

Purpose of the Study:

• To develop a computational framework, InFinity 1.0, to enhance accessibility in protein engineering.
• To address the limitations of resources and timelines in academic synthetic biology competitions.
• To increase awareness and utilization of in silico tools for protein design.

Main Methods:

• Development of the InFinity 1.0 computational framework.
• Focus on simplifying complex protein engineering workflows.
• Adaptation for use within the constraints of the iGEM competition.

Main Results:

• Creation of InFinity 1.0, a framework designed for user-friendliness.
• Demonstrated potential to streamline protein engineering processes.
• Facilitated the development of novel protein functionalities by a student team.

Conclusions:

• InFinity 1.0 offers a pathway to democratize protein engineering.
• Computational tools can be made more accessible for synthetic biology research and education.
• The framework has the potential to broaden participation in advanced protein design projects.