Several computational tools and algorithms are commonly used in enzyme design:
Rosetta: A suite of software for protein modeling and design, widely used for predicting protein structures and designing new enzymes. Molecular Dynamics (MD): Simulations that provide insights into the flexibility and dynamics of enzyme structures. Quantum Mechanics/Molecular Mechanics (QM/MM): Hybrid methods that combine quantum mechanical and molecular mechanical calculations to accurately model enzyme catalysis. Machine Learning: Algorithms that can predict the effects of mutations on enzyme activity based on large datasets.
