2D molecular graphics: a flattened world of chemistry and biology. - Peng Zhou 003; Zhicai Shang (Briefings Bioinform., 2009)

Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities. - Peng Zhou 003; Xiang Chen; Zhicai Shang (J. Comput. Aided Mol. Des., 2009)

2D depiction of nonbonding interactions for protein complexes. - Peng Zhou 003; Feifei Tian; Zhicai Shang (J. Comput. Chem., 2009)

Fluorine Bonding - How Does It Work In Protein-Ligand Interactions? - Peng Zhou 003; Jianwei Zou; Feifei Tian; Zhicai Shang (J. Chem. Inf. Model., 2009)

Systematic Classification and Analysis of Themes in Protein-DNA Recognition. - Peng Zhou 003; Feifei Tian; Yanrong Ren; Zhicai Shang (J. Chem. Inf. Model., 2010)

Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses. - Feifei Tian; Yonggang Lv; Peng Zhou 003; Li Yang 002 (J. Comput. Aided Mol. Des., 2011)

Fast and reliable prediction of domain-peptide binding affinity using coarse-grained structure models. - Feifei Tian; Rui Tan; Tailin Guo; Peng Zhou 003; Li Yang 002 (Biosyst., 2013)

Epitope Mapping of Metuximab on CD147 Using Phage Display and Molecular Docking. - Bifang He; Canquan Mao; Beibei Ru; Hesong Han; Peng Zhou 003; Jian Huang 004 (Comput. Math. Methods Medicine, 2013)

Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity. - Peng Zhou 003; Congcong Wang; Feifei Tian; Yanrong Ren; Chao Yang 023; Jian Huang 004 (J. Comput. Aided Mol. Des., 2013)

Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition. - Hua Yu; Peng Zhou 003; Maolin Deng; Zhicai Shang (J. Chem. Inf. Model., 2014)

Self-Binding Peptides: Folding or Binding? - Chao Yang 023; Shilei Zhang; Ping He; Congcong Wang; Jian Huang 004; Peng Zhou 003 (J. Chem. Inf. Model., 2015)

BDB: biopanning data bank. - Bifang He; Guoshi Chai; Yaocong Duan; Zhiqiang Yan; Liuyang Qiu; Huixiong Zhang; Zechun Liu; Qiang He; Ke Han; Beibei Ru; Feng-Biao Guo; Hui Ding 005; et al. (Nucleic Acids Res., 2016)

Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c-Src. - Zhengya Bai; Shasha Hou; Shilei Zhang; Zhongyan Li; Peng Zhou 003 (J. Chem. Inf. Model., 2017)

Occlusion-Adaptive Deep Network for Robust Facial Expression Recognition. - Hui Ding 002; Peng Zhou 003; Rama Chellappa (IJCB, 2020)

Use of Gaussian Process to Model, predict and Explain Human Emotional response to Chinese Traditional Music. - Jun Su; Peng Zhou 003 (Adv. Complex Syst., 2021)

Systematic Comparison and Comprehensive Evaluation of 80 Amino Acid Descriptors in Peptide QSAR Modeling. - Peng Zhou 003; Qian Liu; Ting Wu; Qingqing Miao; Shuyong Shang; Heyi Wang; Zheng Chen; Shaozhou Wang; Heyan Wang (J. Chem. Inf. Model., 2021)

Integrated unsupervised-supervised modeling and prediction of protein-peptide affinities at structural level. - Peng Zhou 003; Li Wen; Jing Lin; Li Mei; Qian Liu; Shuyong Shang; Juelin Li; Jianping Shu (Briefings Bioinform., 2022)

Machine Learning-based Modeling and Prediction of the Intrinsic Relationship between Human Emotion and Music. - Jun Su; Peng Zhou 003 (ACM Trans. Appl. Percept., 2022)

Musical protein: Mapping the time sequence of music onto the spatial architecture of proteins. - Jun Su; Peng Zhou 003 (Comput. Methods Programs Biomed., 2024)

MV2MAE: Multi-View Video Masked Autoencoders. - Ketul Shah; Robert Crandall; Jie Xu; Peng Zhou 003; Marian George; Mayank Bansal; Rama Chellappa (CoRR, 2024)

The C-terminal self-binding helical peptide of human estrogen-related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists. - Zilong Li; Yue Peng; Haiyang Ye; Yunyi Zhang; Peng Zhou 003 (J. Comput. Chem., 2024)

Rational molecular design of novel class-III peptidic antagonists to competitively disrupt human PPARδ self-binding peptide. - Yue Peng; Zilong Li; Yunyi Zhang; Haiyang Ye; Li Mei; Shuyong Shang; Peng Zhou 003 (J. Comput. Aided Mol. Des., 2025)