Yaoqi Zhou

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 56

Top Topics

Protein Structure

Solvent Accessibility

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Briefings Bioinform.

Publications

Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou
MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search. Genom. Proteom. Bioinform. 22 (1) (2024)
Yidong Song, Qianmu Yuan, Sheng Chen, Ken Chen, Yaoqi Zhou, Yuedong Yang
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. Briefings Bioinform. 24 (4) (2023)
Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning. Briefings Bioinform. 24 (1) (2023)
Xing Zhang, Hongmei Yin, Fei Ling, Jian Zhan, Yaoqi Zhou
SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network. PLoS Comput. Biol. 19 (12) (2023)
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, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan
Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Briefings Bioinform. 23 (3) (2022)
Jaswinder Singh, Kuldip K. Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. Bioinform. 38 (16) (2022)
Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou
SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model. Bioinform. 38 (7) (2022)
Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip K. Paliwal, Yaoqi Zhou
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis. Bioinform. 37 (20) (2021)
Jaspreet Singh, Jaswinder Singh, Kuldip K. Paliwal, Andrew Busch, Yaoqi Zhou
SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks. CIBCB (2021)
Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou
RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks. J. Chem. Inf. Model. 61 (6) (2021)
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, Yaoqi Zhou, Lukasz A. Kurgan
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 49 (Database-Issue) (2021)
Shide Liang, Zhixiu Li, Jian Zhan, Yaoqi Zhou
De novo protein design by an energy function based on series expansion in distance and orientation dependence. Bioinform. 38 (1) (2021)
Anil Kumar Hanumanthappa, Jaswinder Singh, Kuldip K. Paliwal, Jaspreet Singh, Yaoqi Zhou
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network. Bioinform. 36 (21) (2021)
Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang
DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM (2021)
Qianmu Yuan, Jianwen Chen, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinform. 38 (1) (2021)
Jaspreet Singh, Thomas Litfin, Kuldip Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa, Yaoqi Zhou
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. Bioinform. 37 (20) (2021)
Jaswinder Singh, Kuldip K. Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin, Yaoqi Zhou
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning. Bioinform. 37 (17) (2021)
Bailing Zhou, Baohua Ji, Kui Liu, Guodong Hu, Fei Wang, Qingshuai Chen, Ru Yu, Pingping Huang, Jing Ren, Chengang Guo, Huiying Zhao, Hongmei Zhang, Dongbo Zhao, Zhiwei Li, Qiangcheng Zeng, Jiafeng Yu, Yunqiang Bian, Zanxia Cao, Shicai Xu, Yuedong Yang, Yaoqi Zhou, Jihua Wang
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 49 (Database-Issue) (2021)
Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou, Yuedong Yang
SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map. J. Comput. Chem. 41 (8) (2020)
Peter Brown, Yaoqi Zhou
Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database J. Biol. Databases Curation 2020 (2020)
Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. Bioinform. 36 (4) (2020)
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. J. Comput. Biol. 27 (5) (2020)
Kai Wang, Nan Lyu, Hongjuan Diao, Shujuan Jin, Tao Zeng, Yaoqi Zhou, Ruibo Wu
GM-DockZn: a geometry matching-based docking algorithm for zinc proteins. Bioinform. 36 (13) (2020)
Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. J. Comput. Biol. 27 (6) (2020)
Tong Wang, Yanhua Qiao, Wenze Ding, Wenzhi Mao, Yaoqi Zhou, Haipeng Gong
Improved fragment sampling for ab initio protein structure prediction using deep neural networks. Nat. Mach. Intell. 1 (8) (2019)
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. Genom. Proteom. Bioinform. 17 (6) (2019)
Pin Chen, Yaobin Ke, Yutong Lu, Yunfei Du, Jiahui Li, Hui Yan, Huiying Zhao, Yaoqi Zhou, Yuedong Yang
DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state. J. Cheminformatics 11 (1) (2019)
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
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. Bioinform. 35 (14) (2019)
Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P. Campbell
SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties. Bioinform. 35 (20) (2019)
Peter Brown, RELISH Consortium, Yaoqi Zhou
Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database J. Biol. Databases Curation 2019 (2019)
Thomas Litfin, Yuedong Yang, Yaoqi Zhou
SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites. J. Chem. Inf. Model. 59 (2) (2019)
Jaswinder Singh, Jack Hanson, Rhys Heffernan, Kuldip K. Paliwal, Yuedong Yang, Yaoqi Zhou
Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning. J. Chem. Inf. Model. 58 (9) (2018)
Ghazaleh Taherzadeh, Yuedong Yang, Hao-Dong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
Predicting lysine-malonylation sites of proteins using sequence and predicted structural features. J. Comput. Chem. 39 (22) (2018)
Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
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. BMC Bioinform. 19 (1) (2018)
Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang
-factor profile prediction for RNA flexibility using support vector machines. J. Comput. Chem. 39 (8) (2018)
Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou
Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures. J. Chem. Inf. Model. 58 (11) (2018)
Yuedong Yang, Jianzhao Gao, Jihua Wang, Rhys Heffernan, Jack Hanson, Kuldip K. Paliwal, Yaoqi Zhou
Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Briefings Bioinform. 19 (3) (2018)
Rhys Heffernan, Kuldip K. Paliwal, James G. Lyons, Jaswinder Singh, Yuedong Yang, Yaoqi Zhou
Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. J. Comput. Chem. 39 (26) (2018)
Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks. Bioinform. 34 (23) (2018)
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
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res. 46 (Database-Issue) (2018)
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
Structure-based prediction of protein- peptide binding regions using Random Forest. Bioinform. 34 (3) (2018)
Rhys Heffernan, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
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. Bioinform. 33 (18) (2017)
Jack Hanson, Yuedong Yang, Kuldip K. Paliwal, Yaoqi Zhou
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks. Bioinform. 33 (5) (2017)
Tong Wang, Yuedong Yang, Yaoqi Zhou, Haipeng Gong
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction. Bioinform. 33 (5) (2017)
Thomas Litfin, Yaoqi Zhou, Yuedong Yang
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library. Bioinform. 33 (8) (2017)
Jia-Feng Yu, Xianghua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. BMC Bioinform. 18 (1) (2017)
Peter Brown, Yuedong Yang, Yaoqi Zhou, Wayne J. Pullan
A heuristic for the time constrained asymmetric linear sum assignment problem. J. Comb. Optim. 33 (2) (2017)
Yuedong Yang, Yaoqi Zhou
Effective protein conformational sampling based on predicted torsion angles. J. Comput. Chem. 37 (11) (2016)
Md. Tamjidul Hoque, Yuedong Yang, Avdesh Mishra, Yaoqi Zhou
sDFIRE: Sequence-specific statistical energy function for protein structure prediction by decoy selections. J. Comput. Chem. 37 (12) (2016)
Ghazaleh Taherzadeh, Yuedong Yang, Tuo Zhang, Alan Wee-Chung Liew, Yaoqi Zhou
Sequence-based prediction of protein-peptide binding sites using support vector machine. J. Comput. Chem. 37 (13) (2016)
Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinform. 32 (3) (2016)
Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. Bioinform. 32 (6) (2016)
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines. J. Chem. Inf. Model. 56 (10) (2016)
Jianzhao Gao, Yuedong Yang, Yaoqi Zhou
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. Bioinform. 32 (24) (2016)
Yuedong Yang, Jian Zhan, Yaoqi Zhou
SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity. J. Comput. Chem. 37 (18) (2016)
Lukas Folkman, Yuedong Yang, Zhixiu Li, Bela Stantic, Abdul Sattar, Matthew E. Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou
DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinform. 31 (10) (2015)
James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, Alok Sharma, Kuldip K. Paliwal, Abdul Sattar, Yaoqi Zhou, Yuedong Yang
Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network. J. Comput. Chem. 35 (28) (2014)
Shide Liang, Chi Zhang, Yaoqi Zhou
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. J. Comput. Chem. 35 (4) (2014)
Huiying Zhao, Yuedong Yang, Mark von Itzstein, Yaoqi Zhou
Carbohydrate-binding protein identification by coupling structural similarity searching with binding affinity prediction. J. Comput. Chem. 35 (30) (2014)
Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, Yaoqi Zhou
SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J. Comput. Chem. 33 (3) (2012)
Yuedong Yang, Eshel Faraggi, Huiying Zhao, Yaoqi Zhou
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. Bioinform. 27 (15) (2011)
Shide Liang, Yaoqi Zhou, Nick V. Grishin, Daron M. Standley
Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. J. Comput. Chem. 32 (8) (2011)
Marcin J. Mizianty, Tuo Zhang, Bin Xue, Yaoqi Zhou, A. Keith Dunker, Vladimir N. Uversky, Lukasz A. Kurgan
In-silico prediction of disorder content using hybrid sequence representation. BMC Bioinform. 12 (2011)
Huiying Zhao, Yuedong Yang, Yaoqi Zhou
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function. Bioinform. 26 (15) (2010)
Hongzhi Li, Yaoqi Zhou
SCUD: Fast structure clustering of decoys using reference state to remove overall rotation. J. Comput. Chem. 26 (11) (2005)
Hongyi Zhou, Yaoqi Zhou
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures. Bioinform. 21 (18) (2005)
Hongzhi Li, Yaoqi Zhou
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function. J. Bioinform. Comput. Biol. 3 (5) (2005)
Hongyi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou
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. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)