Selected publications
You can also find my other publications on my Google Scholar profile.
Published in Nature Communications, 2023
In this work, we developed trRosettaRNA, a deep learning-based RNA structure prediction method. The blind tests of the CASP15 and the RNA-Puzzles experiments show that the automated trRosettaRNA is promising to advance RNA structure prediction.
Reference: Wenkai Wang#, Chenjie Feng#, Renmin Han#, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang, Zhenling Peng, Jianyi Yang. "trRosettaRNA: automated prediction of RNA 3D structure with transformer network." Nature Communications. 14: 7266 (2023). https://www.nature.com/articles/s41467-023-42528-4
Published in Nature Computational Science, 2022
In this article, we introduce trRosettaX-Single, a deep learning-based single-sequence protein structure prediction method with a supervised transformer protein language model. Benchmark tests show that our method outperforms AlphaFold2 and RoseTTAFold on orphan proteins. As a demonstration, trRosettaX-Single is applied to protein design/hallucination and missense mutation analysis.
Reference: Wenkai Wang, Zhenling Peng, Jianyi Yang*, Single-sequence protein structure prediction using supervised transformer protein language models. Nature Computational Science, 2: 804-814 (2022). https://www.nature.com/articles/s43588-022-00373-3
Published in Advanced Science, 2021
In this work, trRosettaX, an improved version of trRosetta for protein structure prediction is presented. A preliminary version of trRosettaX is ranked as one of the top server groups in CASP14 blind test. Additional benchmark test on 161 targets from CAMEO shows that trRosettaX outperforms the top groups in CAMEO.
Reference: Hong Su#, Wenkai Wang#, Zongyang Du, Zhenling Peng, Shang-Hua Gao, Ming-Ming Cheng, Jianyi Yang*. (2021). "Improved protein structure prediction using a new multi‐scale network and homologous templates." Advanced Science. 2021, 8, 2102592. https://doi.org/10.1002/advs.202102592
