article · Communications Chemistry · 2023
Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15
Jian Liu, Zhiye Guo, Tianqi Wu, Raj S. Roy, Chen Chen, Jianlin Cheng
Cited by 29Open access
Abstract
Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.
Cite this paper
Liu, J., Guo, Z., Wu, T., Roy, R. S., Chen, C., & Cheng, J. (2023). Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15. Communications Chemistry, 6(1), 188. https://doi.org/10.1038/s42004-023-00991-6
Liu, Jian, et al. “Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15.” Communications Chemistry, vol. 6, no. 1, 2023, p. 188, https://doi.org/10.1038/s42004-023-00991-6.
Liu, Jian, Zhiye Guo, Tianqi Wu, Raj S. Roy, Chen Chen, and Jianlin Cheng. 2023. “Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15.” Communications Chemistry 6 (1): 188. https://doi.org/10.1038/s42004-023-00991-6.
Liu, J. et al. (2023) ‘Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15’, Communications Chemistry, 6(1), p. 188. Available at: https://doi.org/10.1038/s42004-023-00991-6.
@article{liu2023improving,
title = {{Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15}},
author = {Liu, Jian and Guo, Zhiye and Wu, Tianqi and Roy, Raj S. and Chen, Chen and Cheng, Jianlin},
journal = {Communications Chemistry},
volume = {6},
number = {1},
pages = {188},
year = {2023},
doi = {10.1038/s42004-023-00991-6}
}Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.