Structure-informed Language Models Are Protein Designers
This addresses the challenge of protein design for researchers in computational biology, offering a novel hybrid approach that improves state-of-the-art results.
The paper tackles the problem of designing protein sequences for given folds by introducing LM-Design, a method that reprograms sequence-based protein language models to incorporate structural awareness, resulting in up to 4% to 12% accuracy gains in sequence recovery, such as 55.65% on CATH 4.2 benchmarks.
This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)