Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms

Artificial intelligence (AI) has transformed protein engineering by leveraging deep learning, protein language models, and knowledge graphs to decode relationships between sequence, structure, and function. Models like AlphaFold2 achieve near-experimental accuracy in structure prediction, while transformer-based language models facilitate de novo sequence design under functional constraints. AI enhances therapeutic protein engineering, enzyme catalysis, and synthetic biology, accelerating the transition from in silico design to experimental validation. These advances accelerate experimental validation across healthcare and industrial biotechnology. Despite algorithmic successes, challenges remain in model interpretability, training data biases, and experimental validation rates. This review examines the computational methodologies shaping protein design, benchmarking metrics, and the integration of machine learning with experimental pipelines.