The xxuLAB
for biomolecular structure prediction and modeling
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The xxuLAB for biomolecular structure prediction and modeling |
[6] Wang, K.; Yin, Z.; Sang, C.; Xia, W.; Wang, Y.; Sun, T.; Xu, X. Geometric deep learning for the prediction of magnesium-binding sites in RNA structures. Int. J. Biol. Macromol. 2024, 262, 130150.
[5] Wang, F.; Xia, R.; Su, Y.; Cai, P.; Xu, X. Quantifying RNA structures and interactions with a unified reduced chain representation model. Int. J. Biol. Macromol. 2023, 253, 127181.
[4] Xu, X.; Jin, L.; Xie, L.; Chen, S.-J. Landscape zooming toward the prediction of RNA cotranscriptional folding. J. Chem. Theory Comput. 2022, 18, 2002-2015.
[3] Xu, X.; Chen, S.-J. Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction. Nucleic Acids Res. 2020, 48, 6503-6512.
[2] Xu, X.; Yu, T.; Chen, S.-J. Understanding the kinetic mechanism of RNA single base pair formation. Proc. Natl. Acad. Sci. USA 2016, 113, 116-121.
[1] Xu, X.; Chen, S.-J. Kinetic mechanism of conformational switch between bistable RNA hairpins. J. Am. Chem. Soc. 2012, 134, 12499-12507.
[4] Xu, X.; Chen, S.-J. Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA. In: Ponchon, L. (eds) RNA Scaffolds. Methods in Mol. Biol. 2021, 2323, 1-11.
[3] Zhao, C.; Xu, X.; Chen, S.-J. Predicting RNA Structure with Vfold. In: Kaufmann, M., Klinger, C., Savelsbergh, A. (eds) Functional Genomics. Methods in Mol. Biol. 2017, 1654, 3-15.
[2] Xu, X.; Chen, S.-J. A Method to Predict the Structure and Stability of RNA/RNA Complexes. In: Turner, D., Mathews, D. (eds) RNA Structure Determination. Methods in Mol. Biol. 2016, 1490, 63-72.
[1] Xu, X.; Chen, S.-J. A Method to Predict the 3D Structure of an RNA Scaffold. In: Ponchon, L. (eds) RNA Scaffolds. Methods in Mol. Biol. 2015, 1316, 1-11.