Yaoqi Zhou

发表

SP5: Improving Protein Fold Recognition by Using Torsion Angle Profiles and Profile-Based Gap Penalty Model

Wei Zhang, Song Liu, Yaoqi Zhou, 2008, PloS one.

A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2012, Proteins.

Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets

Yaoqi Zhou, Yuedong Yang, Huiying Zhao, 2010, Nucleic acids research.

Quantifying the effect of burial of amino acid residues on protein stability

Hongyi Zhou, Yaoqi Zhou, 2003, Proteins.

Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction

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

An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state

Hongyi Zhou, Song Liu, Yaoqi Zhou, 2004, Protein science : a publication of the Protein Society.

Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition

Hongyi Zhou, Yaoqi Zhou, 2004, Proteins.

Interpreting the folding kinetics of helical proteins

M. Karplus, Yaoqi Zhou, 1999, Nature.

Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2017, PloS one.

Protein binding site prediction using an empirical scoring function

Song Liu, Yaoqi Zhou, Chi Zhang, 2006, Nucleic acids research.

Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential

Song Liu, Yaoqi Zhou, Chi Zhang, 2004, Protein science : a publication of the Protein Society.

Specific interactions for ab initio folding of protein terminal regions with secondary structures

Yaoqi Zhou, Yuedong Yang, 2008, Proteins.

Improving computational protein design by using structure‐derived sequence profile

Yaoqi Zhou, Yuedong Yang, Liang Dai, 2010, Proteins.

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes.

Song Liu, Yaoqi Zhou, Qianqian Zhu, 2005, Journal of medicinal chemistry.

A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding

Hongyi Zhou, Song Liu, Yaoqi Zhou, 2004, Proteins.

Energy functions in de novo protein design: current challenges and future prospects.

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2013, Annual review of biophysics.

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.

Unbound Protein-Protein Docking Selections by the DFIRE-based Statistical Pair Potential

Song Liu, Yaoqi Zhou, Chi Zhang, 2004, q-bio/0406025.

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.

Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation.

Yaoqi Zhou, Huiying Zhao, D. Cooper, 2014, Human molecular genetics.

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

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

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

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

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.

Thermodynamics of an All-Atom Off-Lattice Model of the Fragment B of Staphylococcal Protein A: Implication for the Origin of the Cooperativity of Protein Folding

Yaoqi Zhou, A. Linhananta, 2002 .

Real-time reliable determination of binding kinetics of DNA hybridization using a multi-channel graphene biosensor

Yaoqi Zhou, J. Zhan, Jihua Wang, 2017, Nature Communications.

) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment N Sequences

Hongyi Zhou, Yaoqi Zhou, 2005 .

( N – 1 ) / 2 Pairwise Alignments Consistency – based Refinement Guide Tree Building Progressive Multiple Alignment Global Multiple Alignment

Hongyi Zhou, Yaoqi Zhou, 2005 .

Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning

James G. Lyons, K. Paliwal, Yaoqi Zhou, 2015, Scientific Reports.

The dependence of all-atom statistical potentials on structural training database.

Hongyi Zhou, Song Liu, Yaoqi Zhou, 2004, Biophysical journal.

What is a desirable statistical energy functions for proteins and how can it be obtained?

Hongyi Zhou, Song Liu, Yaoqi Zhou, 2007, Cell Biochemistry and Biophysics.

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions

Yaoqi Zhou, Yuedong Yang, 2008, Protein science : a publication of the Protein Society.

Experimentally Validated Plant lncRNAs in EVLncRNAs Database.

Yaoqi Zhou, Jia-Feng Yu, Yuedong Yang, 2019, Methods in molecular biology.

Folding rate prediction using total contact distance.

Hongyi Zhou, Yaoqi Zhou, 2002, Biophysical journal.

Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulations of systems with square-well interactions

M. Karplus, Yaoqi Zhou, C. Hall, 1997 .

Protein folding pathways and kinetics: molecular dynamics simulations of beta-strand motifs.

Yaoqi Zhou, C. Hall, H. Jang, 2002, Biophysical journal.

Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models.

Yaoqi Zhou, C. Hall, H. Jang, 2004, Biophysical journal.

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

Yaoqi Zhou, Yuedong Yang, Ying Xu, 2017, Scientific Reports.

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.

Real‐value prediction of backbone torsion angles

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

Natural protein sequences are more intrinsically disordered than random sequences

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

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

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

Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile.

Yaoqi Zhou, A. Kloczkowski, M. Kouza, 2017, Methods in molecular biology.

Chapter 10 Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profi le

Yaoqi Zhou, A. Kloczkowski, M. Kouza, 2016 .

Chapter 6 SPIDER 2 : A Package to Predict Secondary Structure , Accessible Surface Area , and Main-Chain Torsional Angles by Deep Neural Networks

James G. Lyons, K. Paliwal, Yaoqi Zhou, 2016 .

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

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

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

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

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.

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.

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.

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.

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.

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.

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

Yaoqi Zhou, Yuedong Yang, Song Liu, 2012, Protein science : a publication of the Protein Society.

Trends in template/fragment-free protein structure prediction

Y. Duan, Yaoqi Zhou, Yuedong Yang, 2010, Theoretical chemistry accounts.

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

Yaoqi Zhou, Yuedong Yang, H. Gong, 2017 .

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.

Fold recognition by concurrent use of solvent accessibility and residue depth

Song Liu, Yaoqi Zhou, Chi Zhang, 2007, Proteins.

Structural insights into the histone H1-nucleosome complex

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

Fluids inside a pore—an integral-equation approach: II. Cylindrical pores

Yaoqi Zhou, G. Stell, 1989 .

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.

SPIN 2 : Predicting sequence profiles from protein structures using deep neural networks

James G. Lyons, K. Paliwal, Yaoqi Zhou, 2018 .

YesU from Bacillus subtilis preferentially binds fucosylated glycans

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2018, Scientific Reports.

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

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

A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions

Yaoqi Zhou, Yuedong Yang, K. Seib, 2018, Nucleic acids research.

Different effects of cholesterol on membrane permeation of arginine and tryptophan revealed by bias-exchange metadynamics simulations.

Yaoqi Zhou, Jihua Wang, Z. Cao, 2019, The Journal of chemical physics.

Bias-Exchange Metadynamics Simulation of Membrane Permeation of 20 Amino Acids

Yaoqi Zhou, Yuedong Yang, Jihua Wang, 2018, International journal of molecular sciences.

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

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

Performance of in silico tools for the evaluation of p 16 INK 4 a ( CDKN 2 A ) variants in CAGI

J. Gough, S. Brenner, E. Capriotti, 2017 .

RegSNPs-Intron: A computational framework for prioritizing Intronic Single Nucleotide Variants in Human Genetic Disease

Yaoqi Zhou, M. Dolan, D. Cooper, 2019, bioRxiv.

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Michael T. Eadon, Yaoqi Zhou, M. Dolan, 2019, Genome Biology.

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

Yaoqi Zhou, Yuedong Yang, D. Cooper, 2017, Human mutation.

Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity

Yaoqi Zhou, J. Zhan, P. Xiong, 2019, bioRxiv.

Accurate inference of the full base-pairing structure of RNA by deep mutational scanning and covariation-induced deviation of activity

Yaoqi Zhou, J. Zhan, P. Xiong, 2019, Nucleic acids research.

Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment

K. Paliwal, Yaoqi Zhou, Jaspreet Singh, 2021, Scientific Reports.

Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment

K. Paliwal, Yaoqi Zhou, Thomas Litfin, 2022, Scientific reports.

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

Lipika R. Pal, Yaoqi Zhou, P. Radivojac, 2019, Human mutation.

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

Yaoqi Zhou, Yuedong Yang, N. Mantri, 2018, BMC Genomics.

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

Hongyi Zhou, Yaoqi Zhou, B. Xue, 2022 .

Nucleotide Sugar Transporter SLC35 Family Structure and Function

Yaoqi Zhou, J. Tiralongo, C. Day, 2019, Computational and structural biotechnology journal.

Small open reading frames: current prediction techniques and future prospect.

Song Liu, Yaoqi Zhou, Haoyu Cheng, 2011, Current protein & peptide science.

Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives

K. Paliwal, Yaoqi Zhou, J. Zhan, 2022, Briefings Bioinform..

Improved RNA homology detection and alignment by automatic iterative search in an expanded database

K. Paliwal, Yaoqi Zhou, Thomas Litfin, 2022, bioRxiv.

Infectivity of Plasmodium falciparum in Malaria-Naive Individuals Is Related to Knob Expression and Cytoadherence of the Parasite

S. Hoffman, Yaoqi Zhou, J. McCarthy, 2016, Infection and Immunity.

DNA sequence repeats identify numerous Type I restriction‐modification systems that are potential epigenetic regulators controlling phase‐variable regulons; phasevarions

Yaoqi Zhou, M. Jennings, Long Yang, 2019, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Fluids inside a pore: an integral equation approach. III: Water-in-oil microemulsions

Yaoqi Zhou, G. Stell, 1989 .

Chemical association in simple models of molecular and ionic fluids. III: The cavity function

Yaoqi Zhou, G. Stell, 1992 .

Analytical approach to molecular liquids. II. Solvation of ions in molecular fluids

Yaoqi Zhou, G. Stell, 1989 .

Analytical approach to molecular liquids. IV. Solvation dynamics and electron‐transfer reactions

H. Friedman, Yaoqi Zhou, G. Stell, 1989 .

High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5′-OH-end linker and unique 3′-P-end fragments from hydroxyl radical cleavage

Yaoqi Zhou, J. Zhan, Thomas Litfin, 2022, RNA biology.

Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling

K. Paliwal, Yaoqi Zhou, Thomas Litfin, 2022, Bioinform..

Phase separation of ionic fluids: an extended Ebeling-Grigo approach

Yaoqi Zhou, G. Stell, S. Yeh, 1996 .

Robust RNA structure refinement by a nucleobase-centric sampling algorithm coupled with a backbone rotameric and quantum-mechanical-energy-scaled base-base knowledge-based potential.

Yaoqi Zhou, J. Zhan, Ruibo Wu, 2021 .

Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2016, Applied Microbiology and Biotechnology.

Stability scale and atomic solvation parameters extracted from 1023 mutation experiments

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

Reactivation of Dihydroorotate Dehydrogenase-Driven Pyrimidine Biosynthesis Restores Tumor Growth of Respiration-Deficient Cancer Cells.

Yaoqi Zhou, M. Ricchetti, T. Cunha-Oliveira, 2019, Cell metabolism.

The calorimetric criterion for a two‐state process revisited

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

Ion solvation dynamics in an interaction-site model solvent

H. Friedman, Yaoqi Zhou, G. Stell, 1991 .

Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes

Yaoqi Zhou, Yuedong Yang, N. Mantri, 2018, BMC Genomics.

Fluids inside a pore—an integral-equation approach

Yaoqi Zhou, G. Stell, 1989 .

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

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

Investigation the Possibility of Using Peptides with a Helical Repeating Pattern of Hydro-Phobic and Hydrophilic Residues to Inhibit IL-10

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2016, PloS one.

Argonaute proteins: structures and their endonuclease activity

Yaoqi Zhou, J. Zhan, Shujuan Jin, 2021, Molecular Biology Reports.

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..

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..

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

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

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.

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 .

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

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

Criticality of charged systems. II. The binary mixture of hard spheres and ions

Yaoqi Zhou, G. Stell, 1995 .

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

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

Chemical association in simple models of molecular and ionic fluids

Yaoqi Zhou, G. Stell, 1989 .

DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks

Yaoqi Zhou, Yuedong Yang, Pan Zhang, 2021, bioRxiv.

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..

Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes.

Song Liu, Yaoqi Zhou, Chi Zhang, 2006, Human molecular genetics.

Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease

Yaoqi Zhou, J. Zhan, Yingshou Lei, 2021, International Journal of Biological Macromolecules.

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

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

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..

Natural protein sequences are more intrinsically disordered than random sequences

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

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

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

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..

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..

Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016

Roland L. Dunbrack, Colby T. Ford, David T. Jones, 2019, Human mutation.

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

Philip M. Kim, S. Brenner, E. Capriotti, 2019, Human mutation.

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.

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

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

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

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

RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants

Yaoqi Zhou, M. Dolan, D. Cooper, 2019, Genome Biology.

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

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

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..

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..

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..

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

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

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

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

Critical assessment of protein intrinsic disorder prediction

M. Y. Lobanov, David C. Jones, K. Paliwal, 2021, Nature Methods.

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..

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.

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

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

Prediction of Protein Secondary Structure

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

SPARKS 2 and SP3 servers in CASP6

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

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.

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

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

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

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

From “Dark Matter” to “Star”: Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

Yaoqi Zhou, Jihua Wang, Kui Liu, 2021, Frontiers in Plant Science.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

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..

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

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

Machine learning models in protein bioinformatics.

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

Domain graph of Arabidopsis proteome by comparative analysis.

Song Liu, Yaoqi Zhou, Chi Zhang, 2005, Journal of proteome research.

In-silico prediction of disorder content using hybrid sequence representation

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

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

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

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

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

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..

Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model.

Yaoqi Zhou, Zhonglin Luo, Jiandong Ding, 2007, Biophysical journal.

Criticality of Charged Systems: I. the Restricted Primitive Model.

Yaoqi Zhou, G. Stell, S. Yeh, 1995 .

Nonlocal integral‐equation approximations. I. The zeroth order (hydrostatic) approximation with applications

Yaoqi Zhou, G. Stell, 1990 .

The theory of semipermeable vesicles and membranes: An integral‐equation approach. II. Donnan equilibrium

Yaoqi Zhou, G. Stell, 1988 .

Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease

Taha, Yaoqi Zhou, Yuedong Yang, 2020, PloS one.

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.

DEPICTER: intrinsic disorder and disorder function prediction server.

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

Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct hsdS Specificity Genes That Can Switch System Specificity by Recombination

Yaoqi Zhou, M. Jennings, Long Yang, 2020, mSystems.

Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement

Yaoqi Zhou, J. Zhan, Ruibo Wu, 2021, Nature Communications.

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

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

Effective protein conformational sampling based on predicted torsion angles

Yaoqi Zhou, Yuedong Yang, Yaoqi Zhou, 2016, 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..

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.

Folding thermodynamics of model four-strand antiparallel beta-sheet proteins.

Yaoqi Zhou, C. Hall, H. Jang, 2001, Biophysical journal.

Folding Thermodynamics of Model Four-Strand Antiparallel -Sheet Proteins

Yaoqi Zhou, C. Hall, H. Jang, 2002 .

Fast and accurate thermodynamics of square-well systems from umbrella- sampling simulations of hard-sphere systems

Yaoqi Zhou, 2001 .

Solute excluded‐volume effects on the stability of globular proteins: A statistical thermodynamic theory

Yaoqi Zhou, C. Hall, 1998 .

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..

The helix–coil transition revisited

Yaoqi Zhou, Jiandong Ding, Yantao Chen, 2007, Proteins.

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..

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.

Systematic analysis of REBASE identifies numerous Type I restriction-modification systems that contain duplicated, variable hsdS specificity genes that randomly switch methyltransferase specificity by recombination

Yaoqi Zhou, M. Jennings, Long Yang, 2020, bioRxiv.

Self‐derived structure‐disrupting peptides targeting methionine aminopeptidase in pathogenic bacteria: a new strategy to generate antimicrobial peptides

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

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

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

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

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

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

Yaoqi Zhou, Eshel Faraggi, Yaoqi Zhou, 2010 .

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.

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..

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

Yaoqi Zhou, George Stell, Yaoqi Zhou, 1992 .

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.

High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing.

Yaoqi Zhou, J. Zhan, Huijun Zhao, 2022, International journal of biological macromolecules.

Outer-sphere electron-transfer reactions in model molecular solvents : the mean spherical approximation

H. Friedman, Yaoqi Zhou, G. Stell, 1991 .

Note on standard free energy of transfer and partitioning of ionic species between two fluid phases

H. Friedman, Yaoqi Zhou, G. Stell, 1988 .

The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A

Yaoqi Zhou, A. Linhananta, 2002 .

Role of hydrophilic and hydrophobic contacts in folding of the second β‐hairpin fragment of protein G: Molecular dynamics simulation studies of an all‐atom model

Yaoqi Zhou, A. Linhananta, 2002, Proteins.

Electron rearrangement and energy relaxation due to a core hole creation in molecules

Yaoqi Zhou, D. M. Hanson, Yongfeng Zhang, 1992 .

The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

M. Karplus, Yaoqi Zhou, R. Berry, 2002 .

Recent advances in glycoinformatic platforms for glycomics and glycoproteomics.

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

Temperature dependence of the distribution of the first passage time: results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G.

Yaoqi Zhou, Chi Zhang, G. Stell, 2003, Journal of the American Chemical Society.

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

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

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.

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

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

Investigation of weak damage in Al0.25Ga0.75As/GaAs by using RBS/C and Raman spectroscopy

Yaoqi Zhou, Jiao-qing Pan, Xiangdong Liu, 2001 .

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..

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..

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.

Analytical approach to molecular liquids. I. Site–site interaction model using an extended mean‐spherical approximation

Yaoqi Zhou, G. Stell, 1989 .

Microscopic modelling of association

Yaoqi Zhou, G. Stell, 1992 .

Analytical approach to molecular liquids. V. Symmetric dissociative dipolar dumbbells with the bonding length σ/3≤L≤σ/2 and related systems

Yaoqi Zhou, G. Stell, 1993 .

Analytical approach to molecular liquids. III. The Born solvation free energy of two fixed ions in a dipolar solvent

H. Friedman, Yaoqi Zhou, G. Stell, 1989 .

Design and folding of a multidomain protein.

Hongyi Zhou, Yaoqi Zhou, Yawen Bai, 2005, Biochemistry.

Critical nucleation size in the folding of small apparently two‐state proteins

Hongyi Zhou, Yaoqi Zhou, Yawen Bai, 2004, Protein science : a publication of the Protein Society.

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..

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..

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

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

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..

Thermodynamics and stability of a β‐sheet complex: Molecular dynamics simulations on simplified off‐lattice protein models

Yaoqi Zhou, C. Hall, H. Jang, 2004, Protein science : a publication of the Protein Society.

Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water.

M. Karplus, Hongyi Zhou, Yaoqi Zhou, 2003, Journal of molecular biology.

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

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

Nonlocal integral‐equation approximations. II. Lennard‐Jones fluids

Yaoqi Zhou, G. Stell, 1990 .

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.

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..

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..

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

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

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

Yaoqi Zhou, Jia-Feng Yu, Xianghua Dou, 2017, BMC Bioinformatics.

SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model

K. Paliwal, Yaoqi Zhou, Thomas Litfin, 2022, Bioinform..

Resurrecting self-cleaving mini-ribozymes from 40-million-year-old LINE-1 elements in human genome

Yaoqi Zhou, J. Zhan, P. Xiong, 2021, bioRxiv.

Interplay of hydrophobic and hydrophilic interactions in sequence-dependent cell penetration of spontaneous membrane-translocating peptides revealed by bias-exchange metadynamics simulations.

Yaoqi Zhou, Jihua Wang, Guodong Hu, 2020, Biochimica et biophysica acta. Biomembranes.

Protein Structure Prediction

Hongyi Zhou, Yaoqi Zhou, Venkatarajan S. Mathura, 2009 .

YesU from Bacillus subtilis preferentially binds fucosylated glycans

Yaoqi Zhou, Yuedong Yang, J. Zhan, 2018, Scientific Reports.

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.

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.

Molecular Dynamics Simulations of Human Antimicrobial Peptide LL-37 in Model POPC and POPG Lipid Bilayers

Yaoqi Zhou, Jihua Wang, Guodong Hu, 2018, International journal of molecular sciences.

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.

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..

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

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

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..

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

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

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

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

Computational Prediction of N- and O-Linked Glycosylation Sites for Human and Mouse Proteins.

Matthew P. Campbell, Yaoqi Zhou, G. Taherzadeh, 2022, Methods in molecular biology.

Self-Inhibitory Peptides Targeting the Neisseria gonorrhoeae MtrCDE Efflux Pump Increase Antibiotic Susceptibility

Taha, Yaoqi Zhou, J. Zhan, 2021, Antimicrobial agents and chemotherapy.

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

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

Critical assessment of protein intrinsic disorder prediction

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2020, Nature Methods.

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.

Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites

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

Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis.

M. Karplus, Yaoqi Zhou, Y. Zhou, 1999, Journal of molecular biology.

Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state.

M. Karplus, D. Vitkup, Yaoqi Zhou, 1999, Journal of molecular biology.

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

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

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

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

Linear dependence on chain length for the thermodynamic properties of tangent hard-sphere chains

Steven W. Smith, Yaoqi Zhou, C. Hall, 1995 .

Thermodynamic perturbation theory for fused hard‐sphere and hard‐disk chain fluids

Yaoqi Zhou, C. Hall, G. Stell, 1995 .

Fused hard‐sphere chain molecules: Comparison between Monte Carlo simulation for the bulk pressure and generalized Flory theories

Yaoqi Zhou, C. Hall, S. Carrà, 1995 .

Cooperativity inScapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water

M. Karplus, Hongyi Zhou, Yaoqi Zhou, 2006 .

Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana

Yaoqi Zhou, Yuedong Yang, Song Liu, 2012, Protein science : a publication of the Protein Society.

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

Alan Wee-Chung Liew, Yaoqi Zhou, Tuo Zhang, 2016, Journal of Computational Chemistry.

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

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

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

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

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

Yaoqi Zhou, Tuo Zhang, Lukasz Kurgan, 2012, J. Comput. Chem..

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

The theory of semipermeable vesicles and membranes: An integral‐equation approach. I. General formalism and application to a hard‐sphere mixture

Yaoqi Zhou, G. Stell, 1988 .

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Silvio C. E. Tosatto, M. Y. Lobanov, Md. Wasi Ul Kabir, 2023, Nucleic Acids Res..

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

Yaoqi Zhou, Eshel Faraggi, Andrzej Kloczkowski, 2014 .

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

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

Equations of state for hard-sphere fluids

Yaoqi Zhou, G. Stell, 1988 .

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..

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

Hongyi Zhou, Yaoqi Zhou, 2003, Protein science : a publication of the Protein Society.

Folding thermodynamics of a model three-helix-bundle protein.

M. Karplus, Yaoqi Zhou, Y. Zhou, 1997, Proceedings of the National Academy of Sciences of the United States of America.

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

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

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.