Automated Large-Scale File Preparation, Docking, and Scoring: Evaluation of ITScore and STScore Using the 2012 Community Structure-Activity Resource Benchmark. - Sam Z. Grinter; Chengfei Yan; Sheng-You Huang; Lin Jiang; Xiaoqin Zou (J. Chem. Inf. Model., 2013)

Predicting peptide binding sites on protein surfaces by clustering chemical interactions. - Chengfei Yan; Xiaoqin Zou (J. Comput. Chem., 2015)

Iterative Knowledge-Based Scoring Functions Derived from Rigid and Flexible Decoy Structures: Evaluation with the 2013 and 2014 CSAR Benchmarks. - Chengfei Yan; Sam Z. Grinter; Benjamin Ryan Merideth; Zhiwei Ma; Xiaoqin Zou (J. Chem. Inf. Model., 2016)

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. - Koon-Kiu Yan; Galip Gürkan Yardimci; Chengfei Yan; William S. Noble; Mark Gerstein (Bioinform., 2017)

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015. - Xianjin Xu; Chengfei Yan; Xiaoqin Zou (J. Comput. Aided Mol. Des., 2017)

MDockPeP: An ab-initio protein-peptide docking server. - Xianjin Xu; Chengfei Yan; Xiaoqin Zou (J. Comput. Chem., 2018)

Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function. - Yunda Si; Chengfei Yan (Briefings Bioinform., 2021)

Protein complex structure prediction powered by multiple sequence alignments of interologs from multiple taxonomic ranks and AlphaFold2. - Yunda Si; Chengfei Yan (Briefings Bioinform., 2022)

A reproducibility analysis-based statistical framework for residue-residue evolutionary coupling detection. - Yunda Si; Yi Zhang; Chengfei Yan (Briefings Bioinform., 2022)

Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models. - Yunda Si; Chengfei Yan (Briefings Bioinform., 2023)