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Hong-Yi Zhou · SciRah

Researcher profile · Semantic Scholar

Hong-Yi Zhou

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Hong-Yi Zhou — researcher profile on SciRah

h-index: 34
Works: 87
Citations: 4,257

Most-cited papers

Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
Hong-Yi Zhou, Yaoqi Zhou
2002Protein Science957 citations Open access
Semantic Scholar
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.
Hong-Yi Zhou, J. Skolnick
2011Biophysical Journal275 citations Open access
Semantic Scholar
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function
J. Skolnick, Mu Gao, Hong-Yi Zhou, Suresh Singh
2021Journal of Chemical Information and Modeling220 citations Open access
Semantic Scholar
Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition
Hong-Yi Zhou, Yaoqi Zhou
2004Proteins: Structure, Function, and Bioinformatics199 citations
Semantic Scholar
Folding rate prediction using total contact distance.
Hong-Yi Zhou, Yaoqi Zhou
2002Biophysical Journal163 citations Open access
Semantic Scholar
An accurate, residue‐level, pair potential of mean force for folding and binding based on the distance‐scaled, ideal‐gas reference state
Chi Zhang, Song Liu, Hong-Yi Zhou, Yaoqi Zhou
2004Protein Science160 citations Open access
Semantic Scholar
Quantifying the effect of burial of amino acid residues on protein stability
Hong-Yi Zhou, Yaoqi Zhou
2003Proteins: Structure, Function, and Bioinformatics146 citations
Semantic Scholar
Comprehensive prediction of drug-protein interactions and side effects for the human proteome
Hong-Yi Zhou, Mu Gao, J. Skolnick
2015Scientific Reports120 citations Open access
Semantic Scholar
Insights into disease-associated mutations in the human proteome through protein structural analysis
Mu Gao, Hong-Yi Zhou, J. Skolnick
2015Structure117 citations Open access
Semantic Scholar
Ab initio protein structure prediction using chunk-TASSER.
Hong-Yi Zhou, J. Skolnick
2007Biophysical Journal93 citations Open access
Semantic Scholar
SPARKS 2 and SP3 servers in CASP6
Hong-Yi Zhou, Yaoqi Zhou
2005Proteins: Structure, Function, and Bioinformatics83 citations
Semantic Scholar
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden‐Markov‐model‐based method
Hong-Yi Zhou, Yaoqi Zhou
2003Protein Science78 citations Open access
Semantic Scholar
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments
Hong-Yi Zhou, Yaoqi Zhou
2002Proteins: Structure, Function, and Bioinformatics78 citations
Semantic Scholar
Analysis of TASSER‐based CASP7 protein structure prediction results
Hong-Yi Zhou, S. Pandit, Seung Yup Lee, J. Borreguero +3 more
2007Proteins: Structure, Function, and Bioinformatics72 citations Open access
Semantic Scholar
DDOMAIN: Dividing structures into domains using a normalized domain–domain interaction profile
Hong-Yi Zhou, B. Xue, Yaoqi Zhou
2007Protein Science71 citations Open access
Semantic Scholar
Protein structure prediction by pro-Sp3-TASSER.
Hong-Yi Zhou, J. Skolnick
2009Biophysical Journal70 citations Open access
Semantic Scholar
DESTINI: A deep-learning approach to contact-driven protein structure prediction
Mu Gao, Hong-Yi Zhou, J. Skolnick
2019Scientific Reports66 citations Open access
Semantic Scholar
FINDSITEcomb: A threading/structure-based, proteomic-scale virtual ligand screening approach
Hong-Yi Zhou, J. Skolnick
2012Journal of Chemical Information and Modeling63 citations Open access
Semantic Scholar
A knowledge-based approach for predicting gene-disease associations
Hong-Yi Zhou, J. Skolnick
2016Bioinform.57 citations Open access
Semantic Scholar
WeFold: A Coopetition for Protein Structure Prediction
George A. Khoury, A. Liwo, F. Khatib, Hong-Yi Zhou +26 more
2014Proteins: Structure, Function, and Bioinformatics57 citations Open access
Semantic Scholar
What is a desirable statistical energy functions for proteins and how can it be obtained?
Yaoqi Zhou, Hong-Yi Zhou, Chi Zhang, Song Liu
2007Cell Biochemistry and Biophysics54 citations
Semantic Scholar
Utility of the Morgan Fingerprint in Structure-Based Virtual Ligand Screening
Hong-Yi Zhou, J. Skolnick
2024Journal of Physical Chemistry B51 citations Open access
Semantic Scholar
Performance of the Pro-sp3-TASSER Server in CASP8
Hong-Yi Zhou, S. Pandit, J. Skolnick
2009Proteins: Structure, Function, and Bioinformatics48 citations Open access
Semantic Scholar
The dependence of all-atom statistical potentials on structural training database.
Chi Zhang, Song Liu, Hong-Yi Zhou, Yaoqi Zhou
2004Biophysical Journal42 citations Open access
Semantic Scholar
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules
Hong-Yi Zhou, Hong-Nan Cao, J. Skolnick
2018Journal of Chemical Information and Modeling41 citations Open access
Semantic Scholar
Template-based protein structure modeling using TASSERVMT
Hong-Yi Zhou, J. Skolnick
2011Proteins: Structure, Function, and Bioinformatics41 citations Open access
Semantic Scholar
Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential
Hong-Yi Zhou, J. Skolnick
2008Proteins: Structure, Function, and Bioinformatics41 citations Open access
Semantic Scholar
Chemical Space of Escherichia coli Dihydrofolate Reductase Inhibitors: New Approaches for Discovering Novel Drugs for Old Bugs
B. Srinivasan, Sam Tonddast-Navaei, Ambrish Roy, Hong-Yi Zhou +1 more
2018Medicinal research reviews (Print)40 citations Open access
Semantic Scholar
Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures
J. Skolnick, Hong-Yi Zhou, Michal Brylinski
2012Journal of Physical Chemistry B40 citations Open access
Semantic Scholar
MEDICASCY: A Machine Learning Approach for Predicting Small Molecule Drug Side Effects, Indications, Efficacy and Mode of Action
Hong-Yi Zhou, Hong-Nan Cao, Lilya V. Matyunina, Madelyn R. Shelby +3 more
2020Molecular Pharmaceutics39 citations Open access
Semantic Scholar
FINDSITEX: A structure based, small molecule virtual screening approach with application to all identified human GPCRs
Hong-Yi Zhou, J. Skolnick
2012Molecular Pharmaceutics39 citations Open access
Semantic Scholar
Repurposing FDA-approved drugs for anti-aging therapies
T. Snell, R. Johnston, B. Srinivasan, Hong-Yi Zhou +2 more
2016Biogerontology (Dordrecht)36 citations Open access
Semantic Scholar
Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water.
Yaoqi Zhou, Hong-Yi Zhou, M. Karplus
2003Journal of Molecular Biology36 citations
Semantic Scholar
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures
Hong-Yi Zhou, Mu Gao, J. Skolnick
2016PLoS ONE34 citations Open access
Semantic Scholar
marine drugs
Anne Marie Sweeney-Jones, Kerstin Gagaring, Jenya Antonova-Koch, Hong-Yi Zhou +5 more
34 citations
Semantic Scholar
On the possible origin of protein homochirality, structure, and biochemical function
J. Skolnick, Hong-Yi Zhou, Mu Gao
2019Proceedings of the National Academy of Sciences of the United States of America33 citations Open access
Semantic Scholar
Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function
J. Skolnick, Mu Gao, Ambrish Roy, B. Srinivasan +1 more
2015Bioorganic & Medicinal Chemistry Letters33 citations Open access
Semantic Scholar
Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
J. Skolnick, Hong-Yi Zhou, Mu Gao
2013Current Opinion in Structural Biology32 citations Open access
Semantic Scholar
Critical nucleation size in the folding of small apparently two‐state proteins
Yawen Bai, Hong-Yi Zhou, Yaoqi Zhou
2004Protein Science31 citations Open access
Semantic Scholar
The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release
Hong-Nan Cao, Mu Gao, Hong-Yi Zhou, J. Skolnick
2018Communications Biology30 citations Open access
Semantic Scholar
Reprogramming yeast metabolism for customized starch-rich micro-grain through low-carbon microbial manufacturing
Zhihui Shi, Zhaoyu Xu, Weihe Rong, Hongbing Sun +7 more
2025Nature Communications26 citations Open access
Semantic Scholar
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening
Hong-Yi Zhou, Hong-Nan Cao, J. Skolnick
2021Journal of Chemical Information and Modeling26 citations Open access
Semantic Scholar
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders
B. Srinivasan, Hong-Yi Zhou, J. Kubanek, J. Skolnick
2014Journal of Cheminformatics26 citations Open access
Semantic Scholar
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations
Hong-Yi Zhou, Mu Gao, J. Skolnick
2018PLoS ONE23 citations Open access
Semantic Scholar
The dual role of a loop with low loop contact distance in folding and domain swapping
A. Linhananta, Hong-Yi Zhou, Yaoqi Zhou
2002Protein Science23 citations Open access
Semantic Scholar
Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein–Protein Interactions
J. Skolnick, Hong-Yi Zhou
2022Journal of Physical Chemistry B22 citations Open access
Semantic Scholar
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
Hong-Yi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou
2005Nucleic Acids Res.22 citations Open access
Semantic Scholar
Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers
T. Snell, R. Johnston, Amelia B. Matthews, Hong-Yi Zhou +2 more
2018Biogerontology (Dordrecht)20 citations Open access
Semantic Scholar
Improving threading algorithms for remote homology modeling by combining fragment and template comparisons
Hong-Yi Zhou, J. Skolnick
2010Proteins: Structure, Function, and Bioinformatics20 citations Open access
Semantic Scholar
Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic “functional” symptomatology including pain, fatigue and gastrointestinal dysmotility
R. Boles, Holly A. Hornung, Alastair E. Moody, Thomas B. Ortiz +10 more
2015Mitochondrion (Amsterdam. Print)16 citations Open access
Semantic Scholar

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