Yaoqi Zhou

发表

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto‐encoder deep neural network

Kuldip K. Paliwal, James G. Lyons, Abdollah Dehzangi, 2014, J. Comput. Chem..

Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks

Yaoqi Zhou, Yuedong Yang, Jianzhao Gao, 2016, Bioinform..

Erratum to: Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Yaoqi Zhou, Peter Brown, Yaoqi Zhou, 2020, Database J. Biol. Databases Curation.

sDFIRE: Sequence‐specific statistical energy function for protein structure prediction by decoy selections

Yaoqi Zhou, Yuedong Yang, Avdesh Mishra, 2016, J. Comput. Chem..

SPIDER2: A Package to Predict Secondary Structure, Accessible Surface Area, and Main-Chain Torsional Angles by Deep Neural Networks.

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2017, Methods in molecular biology.

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.

Yaoqi Zhou, Hongyi Zhou, Hongyi Zhou, 2005, Bioinformatics.

Sixty-five years of the long march in protein secondary structure prediction: the final stretch?

Kuldip K. Paliwal, Rhys Heffernan, Yaoqi Zhou, 2016, Briefings Bioinform..

QBES: Predicting real values of solvent accessibility from sequences by efficient, constrained energy optimization

Yaoqi Zhou, Song Liu, Chi Zhang, 2006, Proteins.

Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions

Yaoqi Zhou, Nick V. Grishin, Daron M. Standley, 2011, J. Comput. Chem..

SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity

Yaoqi Zhou, Yuedong Yang, Jian Zhan, 2016, J. Comput. Chem..

RELISH-DB a large expert-curated database for benchmarking biomedical literature search.

Yaoqi Zhou, Peter Brown, Yaoqi Zhou, 2019 .

Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network

Yaoqi Zhou, Jaspreet Singh, Kuldip Paliwal, 2020, Bioinform..

Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function

Yaoqi Zhou, Hongzhi Li, Yaoqi Zhou, 2005, J. Bioinform. Comput. Biol..

LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction

Tong Wang, Yaoqi Zhou, Yuedong Yang, 2016, Bioinform..

Carbohydrate‐binding protein identification by coupling structural similarity searching with binding affinity prediction

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2014, J. Comput. Chem..

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

Yaoqi Zhou, Chi Zhang, Shide Liang, 2014, J. Comput. Chem..

SPARKS 2 and SP3 servers in CASP6

Yaoqi Zhou, Hongyi Zhou, Hongyi Zhou, 2005, Proteins.

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

Yaoqi Zhou, Jack Hanson, Kuldip K Paliwal, 2019, Genom. Proteom. Bioinform..

GM-DockZn: a geometry matching-based docking algorithm for zinc proteins

Yaoqi Zhou, Kai Wang, Tao Zeng, 2020, Bioinform..

Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning

Yaoqi Zhou, Yuedong Yang, Jack Hanson, 2020, J. Comput. Biol..

SPINE X: Improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles

Lukasz A. Kurgan, Yaoqi Zhou, Yuedong Yang, 2012, J. Comput. Chem..

DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

Yaoqi Zhou, Feng Zhang, Yu-Jie Sha, 2017, BMC Bioinformatics.

Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning

Yaoqi Zhou, Kuldip Paliwal, Jack Hanson, 2019, Bioinform..

In-silico prediction of disorder content using hybrid sequence representation

Lukasz A. Kurgan, Yaoqi Zhou, Tuo Zhang, 2011, BMC Bioinformatics.

Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training

Yaoqi Zhou, Ofer Dor, Yaoqi Zhou, 2006, Proteins.

An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles

Yaoqi Zhou, Yuedong Yang, Beisi Xu, 2009, Proteins.

DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile

Yaoqi Zhou, Hongyi Zhou, Bin Xue, 2007, Protein science : a publication of the Protein Society.

SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2014, Methods in molecular biology.

Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast.

Yaoqi Zhou, Song Liu, Chi Zhang, 2006, Journal of proteome research.

Faculty Opinions recommendation of Peptide design by optimization on a data-parameterized protein interaction landscape.

Yaoqi Zhou, Yaoqi Zhou, 2018, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method

Yaoqi Zhou, Hongyi Zhou, Hongyi Zhou, 2003 .

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

Yaoqi Zhou, Kuldip Paliwal, Jaswinder Singh, 2019, Nature Communications.

Single‐sequence‐based prediction of protein secondary structures and solvent accessibility by deep whole‐sequence learning

Jaswinder Singh, Kuldip K. Paliwal, James G. Lyons, 2018, J. Comput. Chem..

Predicting lysine‐malonylation sites of proteins using sequence and predicted structural features

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, J. Comput. Chem..

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

Kuldip K. Paliwal, Rhys Heffernan, Yaoqi Zhou, 2017, Bioinform..

Effective protein conformational sampling based on predicted torsion angles

Yaoqi Zhou, Yuedong Yang, Yaoqi Zhou, 2016, J. Comput. Chem..

Faculty Opinions recommendation of Removing T-cell epitopes with computational protein design.

Yaoqi Zhou, Yaoqi Zhou, 2014 .

Recent advances in glycoinformatic platforms for glycomics and glycoproteomics.

Yaoqi Zhou, Matthew P Campbell, Jodie L Abrahams, 2019, Current opinion in structural biology.

Detecting Proline and Non-Proline Cis Isomers in Protein Structures from Sequences Using Deep Residual Ensemble Learning

Rhys Heffernan, Yaoqi Zhou, Yuedong Yang, 2018, J. Chem. Inf. Model..

Structure‐based prediction of protein‐ peptide binding regions using Random Forest

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2018, Bioinform..

Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function

Yaoqi Zhou, Song Liu, Chi Zhang, 2005, Proteins.

A heuristic for the time constrained asymmetric linear sum assignment problem

Yaoqi Zhou, Yuedong Yang, Peter Brown, 2017, J. Comb. Optim..

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2017, Nucleic Acids Res..

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Yaoqi Zhou, Peter Brown, RELISH Consortium, 2019, Database J. Biol. Databases Curation.

Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks

Kuldip K. Paliwal, Yaoqi Zhou, Yuedong Yang, 2018, Bioinform..

DEPICTER: intrinsic disorder and disorder function prediction server.

Yaoqi Zhou, Lukasz Kurgan, Kuldip Paliwal, 2019, Journal of molecular biology.

All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2020, J. Comput. Biol..

SCUD: Fast structure clustering of decoys using reference state to remove overall rotation

Yaoqi Zhou, Hongzhi Li, 2005, J. Comput. Chem..

DLIGAND2: an improved knowledge-based energy function for protein–ligand interactions using the distance-scaled, finite, ideal-gas reference state

Yaoqi Zhou, Yuedong Yang, Yutong Lu, 2019, Journal of Cheminformatics.

Improving protein disorder prediction by deep bidirectional long short‐term memory recurrent neural networks

Yaoqi Zhou, Yuedong Yang, Kuldip Paliwal, 2016, Bioinform..

From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design

Yaoqi Zhou, 2010 .

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

Yaoqi Zhou, Song Liu, Chi Zhang, 2005, Nucleic Acids Res..

Machine learning models in protein bioinformatics.

Yaoqi Zhou, Lukasz Kurgan, Yaoqi Zhou, 2011, Current protein & peptide science.

Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2016, J. Chem. Inf. Model..

Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites

Yaoqi Zhou, Yuedong Yang, Ghazaleh Taherzadeh, 2018, Current protocols in protein science.

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

Yaoqi Zhou, Yuedong Yang, Jianzhao Gao, 2018, BMC Bioinformatics.

RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis

Yaoqi Zhou, Jian Zhan, Kuldip Paliwal, 2020, bioRxiv.

B‐factor profile prediction for RNA flexibility using support vector machines

Yaoqi Zhou, Yuedong Yang, Jian Zhan, 2018, J. Comput. Chem..

Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2010, Bioinform..

Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins

Kuldip K. Paliwal, James G. Lyons, Abdollah Dehzangi, 2016, Bioinform..

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic

Yaoqi Zhou, Yuedong Yang, Peter Brown, 2016, Bioinform..

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

Yaoqi Zhou, Yuedong Yang, Kuldip Paliwal, 2018, Bioinform..

Consensus scoring for enriching near‐native structures from protein–protein docking decoys

Yaoqi Zhou, Shide Liang, Samy O. Meroueh, 2009, Proteins.

SPOT‐ligand 2: improving structure‐based virtual screening by binding‐homology search on an expanded structural template library

Yaoqi Zhou, Yuedong Yang, Thomas Litfin, 2017, Bioinform..

Improving the prediction accuracy of residue solvent accessibility and real‐value backbone torsion angles of proteins by guided‐learning through a two‐layer neural network

Yaoqi Zhou, Bin Xue, Eshel Faraggi, 2009, Proteins.

Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines.

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2016, Journal of chemical information and modeling.

DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels

Yunlong Liu, Abdul Sattar, Yaoqi Zhou, 2015, Bioinform..

Faculty Opinions recommendation of Global analysis of protein folding using massively parallel design, synthesis, and testing.

Yaoqi Zhou, Yaoqi Zhou, 2017 .

Assessing secondary structure assignment of protein structures by using pairwise sequence‐alignment benchmarks

A Keith Dunker, Yaoqi Zhou, Wei Zhang, 2008, Proteins.

Faculty Opinions recommendation of A Bayesian framework that integrates multi-omics data and gene networks predicts risk genes from schizophrenia GWAS data.

Yaoqi Zhou, Huiying Zhao, Huiying Zhao, 2020, Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature.

Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2015, IEEE Transactions on NanoBioscience.

Intrinsic Disorder and Semi-disorder Prediction by SPINE-D.

Yaoqi Zhou, Tuo Zhang, Eshel Faraggi, 2016, Methods in molecular biology.

Accessible surface area of proteins from purely sequence information and the importance of global features

Yaoqi Zhou, Eshel Faraggi, Andrzej Kloczkowski, 2014 .

BEST: Improved Prediction of B-Cell Epitopes from Antigen Sequences

Yaoqi Zhou, Lukasz Kurgan, Jianzhao Gao, 2012, PloS one.

Accurate Single-Sequence Prediction of Protein Intrinsic Disorder by an Ensemble of Deep Recurrent and Convolutional Architectures

Yaoqi Zhou, Kuldip Paliwal, Jack Hanson, 2018, J. Chem. Inf. Model..

Sequence‐based prediction of protein–peptide binding sites using support vector machine

Alan Wee-Chung Liew, Yaoqi Zhou, Yuedong Yang, 2016, J. Comput. Chem..

Improved fragment sampling for ab initio protein structure prediction using deep neural networks

Yaoqi Zhou, Tong Wang, Yanhua Qiao, 2019, Nature Machine Intelligence.

SPIN2: Predicting sequence profiles from protein structures using deep neural networks

James G. Lyons, Abdollah Dehzangi, Rhys Heffernan, 2018, Proteins.

Accurate single‐sequence prediction of solvent accessible surface area using local and global features

Yaoqi Zhou, Andrzej Kloczkowski, Eshel Faraggi, 2014, Proteins.

SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties

Abdollah Dehzangi, Yaoqi Zhou, Matthew P Campbell, 2019, Bioinform..

Prediction of One‐Dimensional Structural Properties Of Proteins by Integrated Neural Networks

Yaoqi Zhou, Eshel Faraggi, Yaoqi Zhou, 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

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2011, Bioinform..

SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites

Yaoqi Zhou, Yuedong Yang, Thomas Litfin, 2019, J. Chem. Inf. Model..