Hongyi Zhou

发表

Comprehensive prediction of drug-protein interactions and side effects for the human proteome

J. Skolnick, Hongyi Zhou, M. Gao, 2015, Scientific Reports.

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.

WeFold: A coopetition for protein structure prediction

Adam Liwo, Yi He, David Baker, 2014, Proteins.

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction.

J. Skolnick, Hongyi Zhou, 2011, Biophysical journal.

Ab initio protein structure prediction using chunk-TASSER.

J. Skolnick, Hongyi Zhou, 2007, Biophysical journal.

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.

Further evidence for the likely completeness of the library of solved single domain protein structures.

J. Skolnick, Hongyi Zhou, M. Brylinski, 2012, The journal of physical chemistry. B.

On the role of physics and evolution in dictating protein structure and function.

J. Skolnick, Hongyi Zhou, M. Gao, 2014, Israel journal of chemistry.

How special is the biochemical function of native proteins?

J. Skolnick, Hongyi Zhou, M. Gao, 2016, F1000Research.

FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2012, Molecular pharmaceutics.

) / 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 .

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.

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis.

J. Skolnick, Hongyi Zhou, M. Gao, 2015, Structure.

Folding rate prediction using total contact distance.

Hongyi Zhou, Yaoqi Zhou, 2002, Biophysical journal.

The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.

Michal Brylinski, Jeffrey Skolnick, Hongyi Zhou, 2011, Journal of structural biology.

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.

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.

Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway.

J. Skolnick, Hongyi Zhou, B. Srinivasan, 2016, Bioorganic & medicinal chemistry.

Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function.

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2015, Bioorganic & medicinal chemistry letters.

Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI cross-talk in diffuse intrinsic pontine glioma

J. Skolnick, Hongyi Zhou, M. Gao, 2020, Scientific Reports.

Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs

J. Skolnick, Hongyi Zhou, Ambrish Roy, 2018, Medicinal research reviews.

On the possible origin of protein homochirality, structure, and biochemical function

J. Skolnick, Hongyi Zhou, M. Gao, 2019, Proceedings of the National Academy of Sciences.

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

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

Repurposing FDA-approved drugs for anti-aging therapies

J. Skolnick, Hongyi Zhou, M. Gao, 2016, Biogerontology.

Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein–Protein Interactions

J. Skolnick, Hongyi Zhou, 2022, The journal of physical chemistry. B.

PHEVIR: an artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases

J. Skolnick, Hongyi Zhou, C. Astore, 2022, Scientific Reports.

Repurposing FDA-approved drugs for anti-aging therapies

J. Skolnick, Hongyi Zhou, M. Gao, 2016, Biogerontology.

Protein structure prediction by pro-Sp3-TASSER.

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2009, Biophysical journal.

Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2008, Proteins.

Stability scale and atomic solvation parameters extracted from 1023 mutation experiments

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

Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens

J. Skolnick, Hongyi Zhou, N. Mojib, 2020, Marine drugs.

AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2021, J. Chem. Inf. Model..

Prediction of severe adverse events, modes of action and drug treatments for COVID-19’s complications

J. Skolnick, Hongyi Zhou, Joshy Jacob, 2021, Scientific Reports.

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.

Tasser‐Based Protein Structure Prediction

Jeffrey Skolnick, Hongyi Zhou, Shashi B. Pandit, 2010 .

PSiFR: an integrated resource for prediction of protein structure and function

Hongyi Zhou, Michal Brylinski, Jeffrey Skolnick, 2010, Bioinform..

Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge

J. Skolnick, Hongyi Zhou, M. Gao, 2020, bioRxiv.

A knowledge-based approach for predicting gene-disease associations

Hongyi Zhou, Jeffrey Skolnick, J. Skolnick, 2016, Bioinform..

DESTINI: A deep-learning approach to contact-driven protein structure prediction

J. Skolnick, Hongyi Zhou, M. Gao, 2019, Scientific Reports.

SPARKS 2 and SP3 servers in CASP6

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

LeMeDISCO: A computational method for large-scale prediction & molecular interpretation of disease comorbidity

J. Skolnick, Hongyi Zhou, B. Ilkowski, 2021, medRxiv.

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release

J. Skolnick, Hongyi Zhou, M. Gao, 2018, Communications Biology.

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release

J. Skolnick, Hongyi Zhou, M. Gao, 2018, Communications Biology.

MEDICASCY: A Machine Learning Approach for Predicting Small Molecule Drug Side Effects, Indications, Efficacy and Mode of Action.

Hongyi Zhou, Jeffrey Skolnick, Hongnan Cao, 2020, Molecular pharmaceutics.

Template‐based protein structure modeling using TASSERVMT

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2012, Proteins.

ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2016, PloS one.

Are predicted protein structures of any value for binding site prediction and virtual ligand screening?

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2013, Current opinion in structural biology.

Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers

J. Skolnick, Hongyi Zhou, M. Gao, 2018, Biogerontology.

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.

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..

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening

Jeffrey Skolnick, Hongyi Zhou, Hongnan Cao, 2021, J. Chem. Inf. Model..

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

Hongyi Zhou, Jeffrey Skolnick, Hongnan Cao, 2018, J. Chem. Inf. Model..

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.

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.

J. Skolnick, K. McKernan, Hongyi Zhou, 2015, Mitochondrion.

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.

Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2017, The journal of physical chemistry. B.

Protein Structure Prediction

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

Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders

Hongyi Zhou, Jeffrey Skolnick, Bharath Srinivasan, 2014, Journal of Cheminformatics.

FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach

Hongyi Zhou, Jeffrey Skolnick, J. Skolnick, 2013, J. Chem. Inf. Model..

Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI cross-talk in diffuse intrinsic pontine glioma

J. Skolnick, Hongyi Zhou, M. Jin, 2020, Scientific Reports.

ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2018, PloS one.

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

Charles L. Brooks, Adrian W. R. Serohijos, John Moult, 2009, Nature Reviews Drug Discovery.

Analysis of TASSER‐based CASP7 protein structure prediction results

Seung Yup Lee, Jeffrey Skolnick, Hongyi Zhou, 2007, Proteins.

E. coli DHFR complex with inhibitor AMPQD

J. Skolnick, Hongyi Zhou, H. Cao, 2018 .

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release

J. Skolnick, Hongyi Zhou, H. Cao, 2018, Communications Biology.

DESTINI: A deep-learning approach to contact-driven protein structure prediction

Hongyi Zhou, Jeffrey Skolnick, Mu Gao, 2019, Scientific Reports.

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

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

Ab initio protein structure prediction using chunk-TASSER.

J. Skolnick, Hongyi Zhou, 2007, Biophysical journal.

WeFold: A coopetition for protein structure prediction

George A. Khoury, Adam K. Sieradzan, Tomasz K. Wirecki, 2014, Proteins.

Improving threading algorithms for remote homology modeling by combining fragment and template comparisons

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2010, Proteins.

J. Skolnick, K. McKernan, Hongyi Zhou, 2015, Mitochondrion.

Bioinformatics Applications Note Structural Bioinformatics Psifr: an Integrated Resource for Prediction of Protein Structure and Function

J. Skolnick, Hongyi Zhou, S. Pandit, 2022 .

LeMeDISCO is a computational method for large-scale prediction & molecular interpretation of disease comorbidity

J. Skolnick, Hongyi Zhou, B. Ilkowski, 2022, Communications Biology.

Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs

J. Skolnick, Hongyi Zhou, Ambrish Roy, 2018, Medicinal research reviews.

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.

Atovaquone and Pibrentasvir Inhibit the SARS-CoV-2 Endoribonuclease and Restrict Infection In Vitro but Not In Vivo

J. Skolnick, Hongyi Zhou, Joshy Jacob, 2023, Viruses.