The paper you keep linking literally says they're using a large language model (search for that very string in it).

Sigh. If I start with a pre-trained LLM architecture, and then do extensive further training / fine-tuning with different data and loss functions and custom similarity metrics for specialized search and specialized training procedures, and use feedback from other automated systems, we are far, far more than an LLM. That's the point. Calling something like this an LLM is as deeply misleading as calling AlphaFold an LLM. These tools goes far beyond simple LLMs. The special losses and metrics are really so important here and are why these tools can be so game-changing.