AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues

Ge, L.; Cui, X.; Zhao, K.; Zhou, X.; Zhang, Y.; Zhang, G.

doi:10.1101/2025.07.11.664327

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bioRxiv · 10.1101/2025.07.11.664327

AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues

Ge, L.·Cui, X.·Zhao, K.·Zhou, X.·Zhang, Y.·Zhang, G.

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Abstract

Understanding protein conformational dynamics is critical for elucidating disease mechanisms and facilitating structure-based drug design. While AlphaFold2-based methods have advanced static structure prediction, modeling multiple conformation states with both accuracy and efficiency remains challenging. We present AlphaFlex, an innovative framework that integrates flexible residue prediction with a directed masking strategy for multiple sequence alignments. By selectively relaxing co-evolutionary constraints in dynamic regions, AlphaFlex enables accurate prediction of biologically relevant states while preserving structural fidelity. Benchmarking on 69 apo-holo pairs from the CoDNaS dataset, including enzymes, binding proteins, and chaperones, reveals AlphaFlexs superior performance in both flexible residue identification and multiple conformation prediction. Comparative analysis against AF-Cluster, AF2-conformations, and AlphaFlow demonstrates AlphaFlexs significant advantage, achieving the highest success rate (42%) in accurately predicting apo/holo structures (TM-score >0.95 for both states) while consistently outperforming these methods in reproducing both apo and holo conformations. Notably, AlphaFlex maintains robust performance for membrane proteins, resolving inward- and outward-facing conformations with equal fidelity. Case studies further reveal its unique ability to sample physically plausible intermediate states along transition pathways. These results establish AlphaFlex as a pivotal computational tool for mapping protein conformational landscapes, with promising potential to accelerate structure-based therapeutic development.

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Ge, L., Cui, X., Zhao, K., Zhou, X., Zhang, Y., Zhang, G.. 2025-07-14. AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues. https://doi.org/10.1101/2025.07.11.664327

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