An improved classification of G-protein-coupled receptors using sequence-derived features. - Zhen-Ling Peng; Jianyi Yang 002; Xin Chen 037 (BMC Bioinform., 2010)

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. - Jianyi Yang 002; Zhen-Ling Peng; Xin Chen 037 (BMC Bioinform., 2010)

On the Complementarity of the Consensus-Based Disorder Prediction. - Zhenling Peng; Lukasz A. Kurgan (Pacific Symposium on Biocomputing, 2012)

An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier. - Jiaqi Xia; Zhenling Peng; Dawei Qi; Hongbo Mu; Jianyi Yang 002 (Bioinform., 2017)

A large-scale comparative assessment of methods for residue-residue contact prediction. - Qiqige Wuyun; Wei Zheng 013; Zhenling Peng; Jianyi Yang 002 (Briefings Bioinform., 2018)

mTM-align: an algorithm for fast and accurate multiple protein structure alignment. - Runze Dong; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Bioinform., 2018)

CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction. - Qiaozhen Meng; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2018)

Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method. - Zijuan Zhao; Zhenling Peng; Jianyi Yang 002 (J. Chem. Inf. Model., 2018)

mTM-align: a server for fast protein structure database search and multiple protein structure alignment. - Runze Dong; Shuo Pan; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. - Qi Wu 016; Zhenling Peng; Yang Zhang 040; Jianyi Yang 002 (Nucleic Acids Res., 2018)

Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods. - Hong Su; Mengchen Liu; Saisai Sun; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2019)

Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles. - Saisai Sun; Qi Wu 016; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2019)

CATHER: a novel threading algorithm with predicted contacts. - Zongyang Du; Shuo Pan; Qi Wu 016; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2020)

Protein contact prediction using metagenome sequence data and residual neural networks. - Qi Wu 016; Zhenling Peng; Ivan Anishchenko; Qian Cong; David Baker 001; Jianyi Yang 002 (Bioinform., 2020)

Recognition of small molecule-RNA binding sites using RNA sequence and structure. - Hong Su; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2021)

RNA inter-nucleotide 3D closeness prediction by deep residual neural networks. - Saisai Sun; Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2021)

Improved estimation of model quality using predicted inter-residue distance. - Lisha Ye; Peikun Wu; Zhenling Peng; Jianzhao Gao; Jian Liu; Jianyi Yang 002 (Bioinform., 2021)

Toward the assessment of predicted inter-residue distance. - Zongyang Du; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2022)

Single-sequence protein structure prediction using supervised transformer protein language models. - Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Nat. Comput. Sci., 2022)

On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions. - Yajun Dai; Yang Li 042; Liping Wang; Zhenling Peng; Jianyi Yang 002 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information. - Zhenling Peng; Zixia Li; Qiaozhen Meng; Bi Zhao; Lukasz A. Kurgan (Briefings Bioinform., 2023)

A unified approach to protein domain parsing with inter-residue distance matrix. - Kun Zhu 023; Hong Su; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2023)

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. - Alessio Del Conte; Adel Bouhraoua; Mahta Mehdiabadi; Damiano Clementel; Alexander Miguel Monzon; Alex S. Holehouse; Daniel A. Griffith; Ryan J. Emenecker; Ashwini Patil; Ronesh Sharma; Tatsuhiko Tsunoda; Alok Sharma; et al. (Nucleic Acids Res., 2023)

Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein-ligand Interactions. - Hong Wei; Wenkai Wang; Zhenling Peng; Jianyi Yang 002 (Genom. Proteom. Bioinform., 2024)

RNA threading with secondary structure and sequence profile. - Zongyang Du; Zhenling Peng; Jianyi Yang 002 (Bioinform., 2024)