Current AI for protein engineering relies on small public datasets like the PDB (~10,000 structures), causing models to "hallucinate" or default to known examples. This data bottleneck, orders of magnitude smaller than data used for LLMs, hinders the development of novel therapeutics.
The AI industry is hitting data limits for training massive, general-purpose models. The next wave of progress will likely come from creating highly specialized models for specific domains, similar to DeepMind's AlphaFold, which can achieve superhuman performance on narrow tasks.
To evolve AI from pattern matching to understanding physics for protein engineering, structural data is insufficient. Models need physical parameters like Gibbs free energy (delta-G), obtainable from affinity measurements, to become truly predictive and transformative for therapeutic development.
To break the data bottleneck in AI protein engineering, companies now generate massive synthetic datasets. By creating novel "synthetic epitopes" and measuring their binding, they can produce thousands of validated positive and negative training examples in a single experiment, massively accelerating model development.
Professor Collins’ team successfully trained a model on just 2,500 compounds to find novel antibiotics, despite AI experts dismissing the dataset as insufficient. This highlights the power of cleverly applying specialized AI on modest datasets, challenging the dominant "big data" narrative.
The primary barrier to AI in drug discovery is the lack of large, high-quality training datasets. The emergence of federated learning platforms, which protect raw data while collectively training models, is a critical and undersung development for advancing the field.
While OpenFold trains on public datasets, the pre-processing and distillation to make the data usable requires massive compute resources. This "data prep" phase can cost over $15 million, creating a significant, non-obvious barrier to entry for academic labs and startups wanting to build foundational models.
The progress of AI in predicting cancer treatment is stalled not by algorithms, but by the data used to train them. Relying solely on static genetic data is insufficient. The critical missing piece is functional, contextual data showing how patient cells actually respond to drugs.
The bottleneck for AI in drug development isn't the sophistication of the models but the absence of large-scale, high-quality biological data sets. Without comprehensive data on how drugs interact within complex human systems, even the best AI models cannot make accurate predictions.
A critical weakness of current AI models is their inefficient learning process. They require exponentially more experience—sometimes 100,000 times more data than a human encounters in a lifetime—to acquire their skills. This highlights a key difference from human cognition and a major hurdle for developing more advanced, human-like AI.
The founder of AI and robotics firm Medra argues that scientific progress is not limited by a lack of ideas or AI-generated hypotheses. Instead, the critical constraint is the physical capacity to test these ideas and generate high-quality data to train better AI models.