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Briefings in Bioinformatics|January 17, 2022
A reproducibility analysis-based statistical framework for residue-residue evolutionary coupling detectionYunda Si, Yi Zhang, Chengfei YanBriefings in Bioinformatics|February 9, 2023
Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language modelsYunda Si, Chengfei YanBriefings in Bioinformatics|August 27, 2021
Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss functionYunda Si, Chengfei YanBriefings in Bioinformatics|June 1, 2022
Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2Yunda Si, Chengfei YanElife|April 2, 2024
Protein language model-embedded geometric graphs power inter-protein contact predictionYunda Si, Chengfei YanPlos Computational Biology|September 8, 2025
Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulationsPeng Tao, Yunda Si, Jie Xia, et al.Journal of Computational Chemistry|November 4, 2014
Predicting peptide binding sites on protein surfaces by clustering chemical interactionsChengfei Yan, Xiaoqin ZouStructure (London, England : 1993)|September 20, 2016
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure PredictionChengfei Yan, Xianjin Xu, Xiaoqin ZouJournal of Computer-Aided Molecular Design|July 3, 2017
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015Xianjin Xu, Chengfei Yan, Xiaoqin ZouMethods in Molecular Biology (Clifton, N.J.)|February 26, 2017
The Usage of ACCLUSTER for Peptide Binding Site PredictionChengfei Yan, Xianjin Xu, Xiaoqin ZouPageof 1,802