List of works by Yaoqi Zhou

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

scientific article (publication date: 7 April 2005)

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

scientific article published in November 2007

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

scientific article published on 15 March 2018

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

scientific article published on 9 May 2008

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

article by Jack Hanson et al published 5 November 2018 in Journal of Chemical Information and Modeling

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

scientific article

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

scientific article published on 01 February 2020

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

scholarly article by Jack Hanson published in June 2018

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

scientific article

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

scientific article

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

scientific article published on 20 July 2015

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

scientific article published on 23 October 2019

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

scientific article published on August 2009

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

scientific article

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

scientific article

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

scientific article published on 03 July 2019

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

scientific article published on 01 September 2019

B-factor profile prediction for RNA flexibility using support vector machines.

scientific article published on 21 November 2017

BEST: improved prediction of B-cell epitopes from antigen sequences

scientific article (publication date: 2012)

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

scientific article published on 16 March 2018

Biomedical literature: Testers wanted for article search tool.

scientific article published in September 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

scientific article

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

scientific article published on 15 September 2014

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

scientific article

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

scientific article

Computational Prediction of Carbohydrate-Binding Proteins and Binding Sites

scientific article published on 14 August 2018

Consensus scoring for enriching near-native structures from protein-protein docking decoys

scientific article

Cooperativity in Scapharca Dimeric Hemoglobin: Simulation of Binding Intermediates and Elucidation of the Role of Interfacial Water

scientific article published on 01 February 2003

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

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

scientific article published on 7 January 2015

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

scientific article

DEPICTER: Intrinsic Disorder and Disorder Function Prediction Server

scientific article published on 21 December 2019

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

scientific article published on 07 August 2019

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

scientific article published on 29 August 2018

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

scientific article published on 01 February 2019

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

scientific article

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

scientific article published on 05 April 2017

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

scientific article

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

scientific article published in August 2005

Domain Graph ofArabidopsisProteome by Comparative Analysis

article

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

scientific article published on 21 January 2016

Effective protein conformational sampling based on predicted torsion angles.

scientific article

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

scientific article published on 28 February 2013

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

scientific article published on 12 July 2019

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

scientific article published on 8 September 2016

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

scientific article published on January 2009

Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile

scientific article

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

scientific article published on April 2006

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

scientific article

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

scientific article

Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function.

scientific article published in October 2005

Fold recognition by concurrent use of solvent accessibility and residue depth

scientific article published on 01 August 2007

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

scientific article published in November 1999

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

scientific article published on June 2008

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

scientific article published on December 1997

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

scientific article

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

scientific article published on 30 August 2019

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

scientific article published in February 2018

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

scientific article

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

scientific article published on 01 February 2020

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

scientific article

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

scientific article

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

scientific article published on 22 December 2016

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

scientific article

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.

scientific article published on March 2009

In-silico prediction of disorder content using hybrid sequence representation

scientific article

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

scientific article published on 05 July 2016

Interpreting the folding kinetics of helical proteins

scientific article published in Nature

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

scientific article published in January 2017

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

scientific article published on 25 June 2017

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

scientific article

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

scientific article

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

scientific article

Machine learning models in protein bioinformatics.

scientific article published in September 2011

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

scientific article published on 13 April 2018

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

scientific article published on 18 June 2020

Natural protein sequences are more intrinsically disordered than random sequences

scientific article published on 22 January 2016

Nucleotide Sugar Transporter SLC35 Family Structure and Function

scientific article published on 07 August 2019

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

scientific article published on 25 May 2016

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

scientific article

Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

scientific article

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

scientific article

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

scientific article published on 26 July 2019

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

scientific article published on 14 May 2018

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

scientific article published on July 2009

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

scientific article published on 22 August 2016

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

scientific article

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

scientific article published on October 2013

Protein binding site prediction using an empirical scoring function

scientific article

Protein flexibility prediction by an all-atom mean-field statistical theory.

scientific article

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

scientific article

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

scientific article

Quantitative mapping of genetic similarity in human heritable diseases by shared mutations

scientific article published on 17 October 2017

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

scientific article published on 27 November 2019

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

scientific article published on 15 November 2018

Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties.

scientific article published in July 2007

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

scientific article published on 21 March 2017

Recent advances in glycoinformatic platforms for glycomics and glycoproteomics

scientific article published on 20 December 2019

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

scientific article

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

scientific article published on 28 November 2019

Role of hydrophilic and hydrophobic contacts in folding of the second beta-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model

scientific article

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

SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model

scientific article published on 04 June 2008

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

scientific article published in January 2017

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

scientific article published on 6 March 2018

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

scientific article published on 2 November 2011

SPINE-D: accurate prediction of short and long disordered regions by a single neural-network based method

scientific article

SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map

scientific article published on 17 December 2019

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

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

scientific article published on 14 February 2019

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

scientific article published on January 2014

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

scientific article

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

scientific article published on 01 October 2019

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

scientific article published on 13 September 2016

Sequence-based prediction of protein-peptide binding sites using support vector machine.

scientific article published on 2 February 2016

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

scientific article

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

scientific article

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

scientific article

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

scientific article published in August 2008

Structural insights into the histone H1-nucleosome complex

scientific article

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

scientific article

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

scientific article

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

scientific article

Structure-based prediction of protein-peptide binding regions using Random Forest.

scientific article published on 26 September 2017

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

scientific article published on 16 March 2017

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.

scientific article published in May 2003

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

scientific article

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

scientific article published on May 2012

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

scientific article

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

article

The helix-coil transition revisited

scientific article published in October 2007

The role of semidisorder in temperature adaptation of bacterial FlgM proteins

scientific article published on December 2013

Thermodynamics and stability of a beta-sheet complex: molecular dynamics simulations on simplified off-lattice protein models

scientific article published in January 2004

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

scientific article published on 31 January 2018

Trends in template/fragment-free protein structure prediction

scientific article

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

scientific article published on 14 March 2006

YesU from Bacillus subtilis preferentially binds fucosylated glycans

scientific article published in Scientific Reports

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

scientific article

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

scientific article published on 5 February 2016

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