Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors. - Laurence Miguet; Ziding Zhang; Maryse Barbier; Martin G. Grigorov (J. Comput. Aided Mol. Des., 2006)

Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. - Yong-Zi Chen; Yu-Rong Tang; Zhi-Ya Sheng; Ziding Zhang (BMC Bioinform., 2008)

DescFold: A web server for protein fold recognition. - Ren-Xiang Yan; Jing-Na Si; Chuan Wang; Ziding Zhang (BMC Bioinform., 2009)

Outer membrane proteins can be simply identified using secondary structure element alignment. - Ren-Xiang Yan; Zhen Chen 009; Ziding Zhang (BMC Bioinform., 2011)

Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments. - Chuan Wang; Ren-Xiang Yan; Xiao-Feng Wang; Jing-Na Si; Ziding Zhang (Comput. Biol. Chem., 2011)

Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. - Zhen Chen 009; Yuan Zhou; Ziding Zhang; Jiangning Song (Briefings Bioinform., 2015)

BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. - Xiaobao Dong; Xiaotian Lu; Ziding Zhang (Database J. Biol. Databases Curation, 2015)

MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins. - Yuan Zhou; Shiping Yang; Tonglin Mao; Ziding Zhang (Database J. Biol. Databases Curation, 2015)

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. - Huan Qi; Zhenhong Jiang; Kang Zhang; Shiping Yang; Fei He; Ziding Zhang (Genom. Proteom. Bioinform., 2018)

Prediction of protein-protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). - Shiwei Ma; Qi Song; Huan Tao; Andrew P. Harrison; Shaobo Wang; Wei Liu 072; Shoukai Lin; Ziding Zhang; Yufang Ai; Huaqin He (Briefings Bioinform., 2019)

Critical assessment and performance improvement of plant-pathogen protein-protein interaction prediction methods. - Shiping Yang; Hong Li; Huaqin He; Yuan Zhou; Ziding Zhang (Briefings Bioinform., 2019)

Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods. - Xianyi Lian; Xiaodi Yang; Jiqi Shao; Fujun Hou; Shiping Yang; Dongli Pan; Ziding Zhang (Quant. Biol., 2020)

Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions. - Xiaodi Yang; Ziding Zhang; Stefan Wuchty (ICAART (2), 2021)

Current status and future perspectives of computational studies on human-virus protein-protein interactions. - Xianyi Lian; Xiaodi Yang; Shiping Yang; Ziding Zhang (Briefings Bioinform., 2021)

HVIDB: a comprehensive database for human-virus protein-protein interactions. - Xiaodi Yang; Xianyi Lian; Chen Fu; Stefan Wuchty; Shiping Yang; Ziding Zhang (Briefings Bioinform., 2021)

Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. - Xiaodi Yang; Shiping Yang; Xianyi Lian; Stefan Wuchty; Ziding Zhang (Bioinform., 2021)

SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network. - Yan Huang; Stefan Wuchty; Yuan Zhou; Ziding Zhang (Briefings Bioinform., 2023)

Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM. - Xiaodi Yang; Stefan Wuchty; Zeyin Liang; Li Ji; Bingjie Wang; Jialin Zhu; Ziding Zhang; Yujun Dong (Briefings Bioinform., 2024)

Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions. - Linyang Jiang; Xiaodi Yang; Xiaokun Guo; Dianke Li; Jiajun Li; Stefan Wuchty; Wenyu Shi; Ziding Zhang (Briefings Bioinform., 2025)