Yaoqi Zhou

发表

Predicting functional long non-coding RNAs validated by low throughput experiments

Yuedong Yang, Bailing Zhou, Jian Zhan, 2019 .

Structure-aware protein-protein interaction site prediction using deep graph convolutional network

Yaoqi Zhou, Qianmu Yuan, Jianwen Chen, 2021, Bioinform..

Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning

Kuldip K. Paliwal, Yaoqi Zhou, Thomas Litfin, 2021, Bioinform..

SPOT-1D2: Improving Protein Secondary Structure Prediction using High Sequence Identity Training Set and an Ensemble of Recurrent and Residual-convolutional Neural Networks

Kuldip K. Paliwal, Yaoqi Zhou, Jaswinder Singh, 2021, 2021 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

De novo protein design by an energy function based on series expansion in distance and orientation dependence

Jian Zhan, Yaoqi Zhou, Zhixiu Li, 2021, Bioinform..

EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments

Yuedong Yang, Huiying Zhao, Guodong Hu, 2020, Nucleic Acids Res..

SPOT-Contact-Single: Improving Single-Sequence-Based Prediction of Protein Contact Map using a Transformer Language Model

Kuldip Paliwal, Yaoqi Zhou, Thomas Litfin, 2021, bioRxiv.

DescribePROT: database of amino acid-level protein structure and function predictions

A Keith Dunker, Zoran Obradovic, Lukasz Kurgan, 2020, Nucleic Acids Res..

RNA Backbone Torsion and Pseudotorsion Angle Prediction Using Dilated Convolutional Neural Networks

Kuldip K. Paliwal, Yaoqi Zhou, Jaswinder Singh, 2021, J. Chem. Inf. Model..

RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis

Kuldip K. Paliwal, Jian Zhan, Yaoqi Zhou, 2021, Bioinform..

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, Kuldip Paliwal, Yaoqi Zhou, 2021, Bioinform..

FreeSASA: An open source C library for solvent accessible surface area calculations

Yaoqi Zhou, Yaoqi Zhou, Simon Mitternacht, 2016, F1000Research.

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

Yuedong Yang, Olivier Lichtarge, Giovanni Minervini, 2017, Human mutation.

EASE-MM: Sequence-Based Prediction of Mutation-Induced Stability Changes with Feature-Based Multiple Models.

Bela Stantic, Lukas Folkman, Abdul Sattar, 2016, Journal of molecular biology.

Prediction of Protein Secondary Structure

Andrzej Kloczkowski, Yaoqi Zhou, Eshel Faraggi, 2017, Methods in Molecular Biology.

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations.

Chun Wu, Hongxing Lei, Yaoqi Zhou, 2008, The Journal of chemical physics.

Discriminating between disease-causing and neutral non-frameshifting micro-INDELs by support vector machines by means of integrated sequence- and structure-based features

Yuedong Yang, Matthew Mort, Yaoqi Zhou, 2013 .

Refining near‐native protein–protein docking decoys by local resampling and energy minimization

Shide Liang, Yaoqi Zhou, Guangce Wang, 2009, Proteins.

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations.

A Keith Dunker, Wei-Lun Hsu, Shide Liang, 2009, Biochemistry.

The role of semidisorder in temperature adaptation of bacterial FlgM proteins.

Yuedong Yang, Yaoqi Zhou, Zanxia Cao, 2013, Biophysical journal.

Protein flexibility prediction by an all‐atom mean‐field statistical theory

Yaoqi Zhou, Yaoqi Zhou, Chi Zhang, 2005, Protein science : a publication of the Protein Society.

Real‐value prediction of backbone torsion angles

Bin Xue, Yaoqi Zhou, Eshel Faraggi, 2008, Proteins.

Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome

Yuedong Yang, Sarath Chandra Janga, Huiying Zhao, 2014, Proteins.

Prediction of RNA binding proteins comes of age from low resolution to high resolution.

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2013, Molecular bioSystems.

Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations.

Yaoqi Zhou, Yaoqi Zhou, Liang Dai, 2011, Journal of molecular biology.

Investigating DNA‐, RNA‐, and protein‐based features as a means to discriminate pathogenic synonymous variants

Yuedong Yang, Bela Stantic, Ping Zhang, 2017, Human mutation.

Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction

Yuedong Yang, Jian Zhan, Yaoqi Zhou, 2017, RNA.

The calorimetric criterion for a two‐state process revisited

Yaoqi Zhou, Martin Karplus, M. Karplus, 1999, Protein science : a publication of the Protein Society.

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

Yuedong Yang, Matthew Mort, Weixing Feng, 2017, Human Genetics.

Intrinsically Semi-disordered State and Its Role in Induced Folding and Protein Aggregation

Yaoqi Zhou, Eshel Faraggi, Zhixiu Li, 2013, Cell Biochemistry and Biophysics.

Predicting functional long non-coding RNAs validated by low throughput experiments

Yuedong Yang, Jian Zhan, Xianghua Dou, 2019, bioRxiv.

Chemical association in simple models of molecular and ionic fluids. II. Thermodynamic properties

Yaoqi Zhou, George Stell, Yaoqi Zhou, 1992 .

Stability scale and atomic solvation parameters extracted from 1023 mutation experiments

Hongyi Zhou, Yaoqi Zhou, Hongyi Zhou, 2002, Proteins.

Charting the Unexplored RNA-binding Protein Atlas of the Human Genome

Yuedong Yang, Sarath Chandra Janga, Heng Zhu, 2000 .

Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

Yuedong Yang, Shesheng Zhang, Yaoqi Zhou, 2009, Structure.

Natural protein sequences are more intrinsically disordered than random sequences

Yuedong Yang, Jia-Feng Yu, Yaoqi Zhou, 2016, Cellular and Molecular Life Sciences.

Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments

Hongyi Zhou, Yaoqi Zhou, Hongyi Zhou, 2004, Proteins.

Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2011, RNA biology.

Fluctuations of backbone torsion angles obtained from NMR‐determined structures and their prediction

Yaoqi Zhou, Eshel Faraggi, Yaoqi Zhou, 2010, Proteins.

Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome

Yuedong Yang, Huiying Zhao, Yaoqi Zhou, 2014, PloS one.

DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels

Yuedong Yang, Matthew Mort, Huiying Zhao, 2013, Genome Biology.

Structural insights into the histone H1-nucleosome complex

Yaoqi Zhou, Yawen Bai, Yuedong Yang, 2013, Proceedings of the National Academy of Sciences.

A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys

Song Liu, Shide Liang, Yaoqi Zhou, 2007, Proteins.

Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations.

Yaoqi Zhou, Zhonglin Luo, Yaoqi Zhou, 2008, The Journal of chemical physics.

Predicting residue–residue contact maps by a two‐layer, integrated neural‐network method

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

Real‐SPINE: An integrated system of neural networks for real‐value prediction of protein structural properties

Yaoqi Zhou, Ofer Dor, Yaoqi Zhou, 2007, Proteins.

Direct prediction of profiles of sequences compatible with a protein structure by neural networks with fragment‐based local and energy‐based nonlocal profiles

Yuedong Yang, Jian Zhan, Yaoqi Zhou, 2014, Proteins.

SPINE-D: Accurate Prediction of Short and Long Disordered Regions by a Single Neural-Network Based Method

A Keith Dunker, Vladimir N Uversky, Bin Xue, 2012, Journal of biomolecular structure & dynamics.

The dual role of a loop with low loop contact distance in folding and domain swapping

Hongyi Zhou, Yaoqi Zhou, Hongyi Zhou, 2002, Protein science : a publication of the Protein Society.