SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. - Hongyi Zhou; Yaoqi Zhou (Bioinform., 2005)

Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function. - Hongzhi Li; Yaoqi Zhou (J. Bioinform. Comput. Biol., 2005)

SCUD: Fast structure clustering of decoys using reference state to remove overall rotation. - Hongzhi Li; Yaoqi Zhou (J. Comput. Chem., 2005)

Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations. - Hongyi Zhou; Chi Zhang 013; Song Liu; Yaoqi Zhou (Nucleic Acids Res., 2005)

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. - Huiying Zhao; Yuedong Yang; Yaoqi Zhou (Bioinform., 2010)

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. - Yuedong Yang; Eshel Faraggi; Huiying Zhao; Yaoqi Zhou (Bioinform., 2011)

In-silico prediction of disorder content using hybrid sequence representation. - Marcin J. Mizianty; Tuo Zhang; Bin Xue; Yaoqi Zhou; A. Keith Dunker; Vladimir N. Uversky; Lukasz A. Kurgan (BMC Bioinform., 2011)

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. - Shide Liang; Yaoqi Zhou; Nick V. Grishin; Daron M. Standley (J. Comput. Chem., 2011)

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. - Eshel Faraggi; Tuo Zhang; Yuedong Yang; Lukasz A. Kurgan; Yaoqi Zhou (J. Comput. Chem., 2012)

LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains. - Shide Liang; Chi Zhang 013; Yaoqi Zhou (J. Comput. Chem., 2014)

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. - James G. Lyons; Abdollah Dehzangi; Rhys Heffernan; Alok Sharma; Kuldip K. Paliwal; Abdul Sattar 001; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2014)

Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. - Huiying Zhao; Yuedong Yang; Mark von Itzstein; Yaoqi Zhou (J. Comput. Chem., 2014)

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. - Lukas Folkman; Yuedong Yang; Zhixiu Li; Bela Stantic; Abdul Sattar 001; Matthew E. Mort; David N. Cooper; Yunlong Liu; Yaoqi Zhou (Bioinform., 2015)

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. - Peter Brown; Wayne Pullan; Yuedong Yang; Yaoqi Zhou (Bioinform., 2016)

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. - Jianzhao Gao; Yuedong Yang; Yaoqi Zhou (Bioinform., 2016)

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. - Rhys Heffernan; Abdollah Dehzangi; James G. Lyons; Kuldip K. Paliwal; Alok Sharma; Jihua Wang; Abdul Sattar 001; Yaoqi Zhou; Yuedong Yang (Bioinform., 2016)

sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. - Md. Tamjidul Hoque; Yuedong Yang; Avdesh Mishra; Yaoqi Zhou (J. Comput. Chem., 2016)

Sequence-based prediction of protein-peptide binding sites using support vector machine. - Ghazaleh Taherzadeh; Yuedong Yang; Tuo Zhang; Alan Wee-Chung Liew; Yaoqi Zhou (J. Comput. Chem., 2016)

Effective protein conformational sampling based on predicted torsion angles. - Yuedong Yang; Yaoqi Zhou (J. Comput. Chem., 2016)

SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. - Yuedong Yang; Jian Zhan; Yaoqi Zhou (J. Comput. Chem., 2016)

Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. - Ghazaleh Taherzadeh; Yaoqi Zhou; Alan Wee-Chung Liew; Yuedong Yang (J. Chem. Inf. Model., 2016)

Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. - Jack Hanson; Yuedong Yang; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2017)

Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility. - Rhys Heffernan; Yuedong Yang; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2017)

SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. - Thomas Litfin; Yaoqi Zhou; Yuedong Yang (Bioinform., 2017)

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. - Tong Wang 014; Yuedong Yang; Yaoqi Zhou; Haipeng Gong (Bioinform., 2017)

DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. - Jia-Feng Yu; Xianghua Dou; Yu-Jie Sha; Chun-Ling Wang; Hong-Bo Wang; Yi-Ting Chen; Feng Zhang; Yaoqi Zhou; Ji-Hua Wang (BMC Bioinform., 2017)

A heuristic for the time constrained asymmetric linear sum assignment problem. - Peter Brown; Yuedong Yang; Yaoqi Zhou; Wayne J. Pullan (J. Comb. Optim., 2017)

Sixty-five years of the long march in protein secondary structure prediction: the final stretch? - Yuedong Yang; Jianzhao Gao; Jihua Wang; Rhys Heffernan; Jack Hanson; Kuldip K. Paliwal; Yaoqi Zhou (Briefings Bioinform., 2018)

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 2018)

Structure-based prediction of protein- peptide binding regions using Random Forest. - Ghazaleh Taherzadeh; Yaoqi Zhou; Alan Wee-Chung Liew; Yuedong Yang (Bioinform., 2018)

Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures. - Jianzhao Gao; Yuedong Yang; Yaoqi Zhou (BMC Bioinform., 2018)

B-factor profile prediction for RNA flexibility using support vector machines. - Ivantha Guruge; Ghazaleh Taherzadeh; Jian Zhan; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2018)

Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. - Rhys Heffernan; Kuldip K. Paliwal; James G. Lyons; Jaswinder Singh; Yuedong Yang; Yaoqi Zhou (J. Comput. Chem., 2018)

Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. - Ghazaleh Taherzadeh; Yuedong Yang; Hao-Dong Xu; Yu Xue 001; Alan Wee-Chung Liew; Yaoqi Zhou (J. Comput. Chem., 2018)

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures. - Jack Hanson; Kuldip K. Paliwal; Yaoqi Zhou (J. Chem. Inf. Model., 2018)

Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. - Jaswinder Singh; Jack Hanson; Rhys Heffernan; Kuldip K. Paliwal; Yuedong Yang; Yaoqi Zhou (J. Chem. Inf. Model., 2018)

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. - Bailing Zhou; Huiying Zhao; Jia-Feng Yu; Chengang Guo; Xianghua Dou; Feng Song; Guodong Hu; Zanxia Cao; Yuanxu Qu; Yuedong Yang; Yaoqi Zhou; Jihua Wang (Nucleic Acids Res., 2018)

Large expert-curated database for benchmarking document similarity detection in biomedical literature search. - Peter Brown; RELISH Consortium; Yaoqi Zhou (Database J. Biol. Databases Curation, 2019)

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (Bioinform., 2019)

SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties. - Ghazaleh Taherzadeh; Abdollah Dehzangi; Maryam Golchin; Yaoqi Zhou; Matthew P. Campbell (Bioinform., 2019)

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yaoqi Zhou (Genom. Proteom. Bioinform., 2019)

DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. - Pin Chen; Yaobin Ke; Yutong Lu; Yunfei Du; Jiahui Li 008; Hui Yan; Huiying Zhao; Yaoqi Zhou; Yuedong Yang (J. Cheminformatics, 2019)

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. - Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Chem. Inf. Model., 2019)

Improved fragment sampling for ab initio protein structure prediction using deep neural networks. - Tong Wang 014; Yanhua Qiao; Wenze Ding; Wenzhi Mao; Yaoqi Zhou; Haipeng Gong (Nat. Mach. Intell., 2019)

Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. - Peter Brown; Yaoqi Zhou (Database J. Biol. Databases Curation, 2020)

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. - Jack Hanson; Thomas Litfin; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2020)

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. - Kai Wang 063; Nan Lyu; Hongjuan Diao; Shujuan Jin; Tao Zeng; Yaoqi Zhou; Ruibo Wu (Bioinform., 2020)

Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. - Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yuedong Yang; Yaoqi Zhou (J. Comput. Biol., 2020)

All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. - Tongchuan Zhang; Guodong Hu; Yuedong Yang; Jihua Wang; Yaoqi Zhou (J. Comput. Biol., 2020)

SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. - Yufeng Cai; Xiongjun Li; Zhe Sun; Yutong Lu; Huiying Zhao; Jack Hanson; Kuldip K. Paliwal; Thomas Litfin; Yaoqi Zhou; Yuedong Yang (J. Comput. Chem., 2020)

DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. - Pan Zhang; Shuangjia Zheng; Jianwen Chen; Yaoqi Zhou; Yuedong Yang (BIBM, 2021)

SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks. - Jaspreet Singh; Jaswinder Singh; Kuldip K. Paliwal; Andrew Busch; Yaoqi Zhou (CIBCB, 2021)

Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. - Anil Kumar Hanumanthappa; Jaswinder Singh; Kuldip K. Paliwal; Jaspreet Singh; Yaoqi Zhou (Bioinform., 2021)

De novo protein design by an energy function based on series expansion in distance and orientation dependence. - Shide Liang; Zhixiu Li; Jian Zhan; Yaoqi Zhou (Bioinform., 2021)

SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning. - Jaspreet Singh; Thomas Litfin; Kuldip K. Paliwal; Jaswinder Singh; Anil Kumar Hanumanthappa; Yaoqi Zhou (Bioinform., 2021)

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. - Jaswinder Singh; Kuldip K. Paliwal; Tongchuan Zhang; Jaspreet Singh; Thomas Litfin; Yaoqi Zhou (Bioinform., 2021)

Structure-aware protein-protein interaction site prediction using deep graph convolutional network. - Qianmu Yuan; Jianwen Chen; Huiying Zhao; Yaoqi Zhou; Yuedong Yang (Bioinform., 2021)

RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. - Tongchuan Zhang; Jaswinder Singh; Thomas Litfin; Jian Zhan; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2021)

RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks. - Jaswinder Singh; Kuldip K. Paliwal; Jaspreet Singh; Yaoqi Zhou (J. Chem. Inf. Model., 2021)

DescribePROT: database of amino acid-level protein structure and function predictions. - Bi Zhao; Akila Katuwawala; Christopher J. Oldfield; A. Keith Dunker; Eshel Faraggi; Jörg Gsponer; Andrzej Kloczkowski; Nawar Malhis; Milot Mirdita; Zoran Obradovic; Johannes Söding; Martin Steinegger; et al. (Nucleic Acids Res., 2021)

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. - Bailing Zhou; Baohua Ji; Kui Liu; Guodong Hu; Fei Wang; Qingshuai Chen; Ru Yu; Pingping Huang; Jing Ren; Chengang Guo; Huiying Zhao; Hongmei Zhang; et al. (Nucleic Acids Res., 2021)

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. - Md. Solayman; Thomas Litfin; Jaswinder Singh; Kuldip K. Paliwal; Yaoqi Zhou; Jian Zhan (Briefings Bioinform., 2022)

SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. - Jaspreet Singh; Thomas Litfin; Jaswinder Singh; Kuldip K. Paliwal; Yaoqi Zhou (Bioinform., 2022)

Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. - Jaswinder Singh; Kuldip K. Paliwal; Thomas Litfin; Jaspreet Singh; Yaoqi Zhou (Bioinform., 2022)

EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. - Bailing Zhou; Maolin Ding; Jing Feng; Baohua Ji; Pingping Huang; Junye Zhang; Xue Yu; Zanxia Cao; Yuedong Yang; Yaoqi Zhou; Jihua Wang (Briefings Bioinform., 2023)

Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. - Yidong Song; Qianmu Yuan; Sheng Chen; Ken Chen 006; Yaoqi Zhou; Yuedong Yang (Briefings 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)

SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network. - Xing Zhang; Hongmei Yin; Fei Ling; Jian Zhan; Yaoqi Zhou (PLoS Comput. Biol., 2023)

MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. - Ke Chen; Thomas Litfin; Jaswinder Singh; Jian Zhan; Yaoqi Zhou (Genom. Proteom. Bioinform., 2024)

A Comparative Review of RNA Language Models. - He Wang; Yikun Zhang; Jie Chen; Jian Zhan; Yaoqi Zhou (CoRR, 2025)