One step forward towards deep-learning protein complex structure prediction by precise multiple sequence alignment construction

Keywords

antibody−antigen interactions / deep-learning / multiple sequence alignments / protein−protein complex structure prediction

References

[1] Wells JA, McClendon CL. Reaching for high-hanging fruit in drug discovery at protein−protein interfaces. Nature. 2007;450(7172):1001-1009.

[2] Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583-589.

[3] Evans R, O'Neill M, Pritzel A, et al. Protein complex prediction with AlphaFold-Multimer. Biorxiv. 2021.

[4] Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Rep Methods. 2021;1:100014.

[5] Zheng W, Wuyun Q, Freddolino PL, Zhang Y. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins Struct Funct Bioinf. 2023;91(12):1684-1703.

[6] Zheng W, Wuyun Q, Li Y, Zhang C, Freddolino PL, Zhang Y. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nat Methods. 2024;21:279-289.

[7] Yang P, Zheng W, Ning K, Zhang Y. Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proc Natl Acad Sci USA. 2021;118(49):e2110828118.

[8] Zhang C, Zheng W, Mortuza SM, Li Y, Zhang Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics. 2020;36(7):2105-2112.

[9] Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: insights from CASP15. Proteins Struct Funct Bioinf. 2023;91(12):1636-1657.

[10] Pearce R, Zhang Y. Deep learning techniques have significantly impacted protein structure prediction and protein design. Curr Opin Struct Biol. 2021;68:194-207.

RIGHTS & PERMISSIONS

2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.