Sampling protein structural token space enables accurate prediction of multiple conformations

Abstract

Protein function is fundamentally mediated by ensembles of distinct metastable states. However, existing methods, such as AlphaFold 3, typically exhibit a bias toward predicting a single dominant state, failing to capture alternative conformations or provide robust metrics for identifying high-quality multi-state conformations. Here, we present MultiStateFold (MSFold), a framework that integrates Parallel Tempering into the discrete structure token space of the ESM3 protein language model. By conceptualizing the model's latent space as an implicit energy landscape, MSFold enables global exploration and barrier crossing, thereby overcoming the local sampling limitations inherent in base generative models. Across a benchmark of 313 multi-conformation pairs, MSFold sets a new performance standard: it achieves the highest success rate in modeling native states and substantially outperforms leading methods, including AlphaFold 3, on challenging alternative conformations, while maintaining competitive accuracy for primary structures. Furthermore, we propose Sequence Log-Likelihood (SLL), a novel confidence metric derived from sequence-structure consistency. Our results demonstrate that SLL offers a modest improvement over standard metrics such as pTM and pLDDT. This work establishes a new paradigm for conformational sampling, bridging classical statistical physics with protein language models.