TTS-Design: Test-Time Compute Scaling for Structure-Guided Protein Design
TL;DR
TTS-Design is proposed, a test-time compute scaling framework that enhances protein sequence design without retraining models or relying on larger training datasets, and can consistently improve sequence recovery and structural reliability across different backbone models, without retraining or increasing model size.
Abstract
Generating protein sequences that reliably fold into target structures is a central challenge in computational biology and protein design. Progress in protein inverse folding (PIF), however, is fundamentally constrained by the scarcity of high-quality structural data, which limits the effectiveness of existing models. In this work, we propose TTS-Design, a test-time compute scaling framework that enhances protein sequence design without retraining models or relying on larger training data. For TTS-Design, its core design is a dedicated inverse folding reward model named IF-RM, which quantitatively evaluates structure–sequence compatibility and enables effective selection among multiple candidate sequences at inference time. By integrating IF-RM into existing PIF models, TTS-Design leverages additional computation during inference stage to explore and refine candidate solutions. Extensive experiments on the CATH 4.2 and CATH 4.3 demonstrate that TTS-Design consistently improves sequence recovery and structural reliability across different backbone models, without retraining or increasing model size. Case studies on real-world proteins further confirm its practical effectiveness. Overall, our results highlight test-time compute scaling as a promising and effective paradigm for advancing protein inverse folding and other scientific problems under data-limited scenarios.