Senior Research Scientist
Ph.D., Tsinghua University, 1993
Center for the Study of Systems Biology
950 Atlantic Drive, Room 2145
Atlanta, GA 30332, Mail Code: 2000
Tel: (404) 407-8976
Fax: (404) 385-7478
hzhou3@mail.gatech.edu
Research Interests
Computational Biophysics and Bioinformatics:
- Development of tools for the prediction of protein structure from sequence
- Prediction of protein-protein, protein-DNA interactions
- Elucidation of protein folding mechanism/pathways
- Equilibrium and dynamic properties of protein binding
Publications
Zhou, H, Skolnick J. Submitted. MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special.
Zhou, H, Edelman B, Skolnick J. 2025. A mode-of-action protein based approach that characterizes the relationships among most major diseases. Scientific Reports: 15, 9668. https://doi.org/10.1038/s41598-025-93377-8. PDF
Skolnick, J, Srinivasan B, Skolnick S, Zhou H. 2025. Entabolons: How metabolites modify the biochemical function of proteins and cause the correlated behavior of proteins in pathways. Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.5c00462. PDF
Zhou, H, Skolnick J. 2024. Utility of the Morgan Fingerprint in Structure-Based Virtual Ligand Screening. J. Phys. Chem. B. 2024: 128(22): 5363–5370. https://doi.org/10.1021/acs.jpcb.4c01875. PDF
Zhou, H, Skolnick J. 2024. FRAGSITE2: A Structure and Fragment Based Approach for Virtual Ligand Screening. Protein Science. 2024; 33(1):e4869. https://doi.org/10.1002/pro.4869. PDF
von Beck, T, Hernandez L M, Zhou H, Floyd K, Suthar M, Skolnick J, Jacob J. 2023. Atovaquone and Pibrentasvir Inhibit the SARS-CoV-2 Endoribonuclease and Restrict Infection In Vitro but Not In Vivo. Viruses 15(9): 1841. https://doi.org/10.3390/v15091841. PDF
Zhou, H, Astore C, Skolnick J. 2022. PHEVIR: An artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases. Sci Rep 12, 20889 (2022). https://doi.org/10.1038/s41598-022-25412-x. PDF
Zhou, H, Skolnick J. 2022. Implications of the essential role of small molecule ligand binding pockets in protein-protein interactions. J. Phys. Chem. B. 126 (36), 6853-6867. doi.org/10.1021/acs.jpcb.2c04525. PDF
Skolnick, J, Gao M, Zhou H, Singh S. 2021. AlphaFold 2: Why it works and its implications for understanding the relationships of protein sequence, structure and function. J. Chem. Inf. Model. 61: 10: 4827-4831. doi: 10.1021/acs.jcim.1c01114. PDF
Astore, C, Zhou H, Ilkowski B, Forness J, Skolnick J. 2022. LeMeDISCO: A computational method for large-scale prediction & molecular interpretation of disease comorbidity. Commun Biol. 5, 87. doi.org/10.1038/s42003-022-03816-9. PDF
Astore, C, Zhou H, Skolnick J. 2021. LeMeDISCO: A computational method for large-scale prediction & molecular interpretation of disease comorbidity. medRxiv 2021.06.28.21259559; doi: https://doi.org/10.1101/2021.06.28.21259559 PDF
*This article is a preprint and has not been certified by peer review.
Astore, C, Zhou H, Jacob J, Skolnick J. 2021. Prediction of severe adverse events, modes of action and drug treatments for COVID-19’s complications. Scientific Reports. 11: 20864. PDF
Zhou, H, Cao H, Skolnick J. 2021. FRAGSITE: A Fragment Based Approach for Virtual Ligand Screening. J Chem Inf Model. 61(4): 2074-2089. doi: 10.1021/acs.jcim.0c01160. PDF
Astore, C, Zhou H, Jacob J, Skolnick J. 2021. MOATAI-VIR – an AI algorithm that predicts severe adverse events and molecular features for COVID-19’s complications. medRxiv 2021.01.29.21250712; doi: https://doi.org/10.1101/2021.01.29.21250712. PDF
*This article is a preprint and has not been certified by peer review.
Sweeney-Jones, AM, Gagaring K, Antonova-Koch J, Zhou H, Mojib N, Soapi K, Skolnick J, McNamara C, Kubanek J. 2020. Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens. Marine Drugs. 18: 167. doi:10.3390/md18030167. PDF
Cao, H, Jin M, Gao M, Zhou H, Tao YJ, Skolnick J. 2020. Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI pathway cross-talk in diffuse intrinsic pontine glioma. Scientific Reports. 10: 6140. doi: 10.1038/s41598-020-63061-0. PDF
Zhou, H, Cao H, Matyunina L, Shelby M, Cassels L, McDonald J, Skolnick, J. 2020. MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy and Modes of Action. Molecular Pharmaceutics. 17(5): 1558-1574. doi: 10.1021/acs.molpharmaceut.9b01248. PDF
Skolnick, J, Zhou H, Gao M. 2019. On the possible origin of protein homochirality, structure and biochemical function. PNAS. 116(52): 26571–26579. https://doi.org/10.1073/pnas.1908241116. PDF
Gao, M, Zhou H, Skolnick J. 2019. DESTINI: A deep-learning approach to contact-driven protein structure prediction. Scientific Reports. 9: 3514. https://doi.org/10.1038/s41598-019-40314-1. PDF
Zhou, H, Cao H, Skolnick J. 2018. FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. Journal of Chemical Information and Modeling. 58(11): 2343-2354 doi: 10.1021/acs.jcim.8b00309. PDF
Cao, H, Gao M, Zhou H, Skolnick J. 2018. The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release. Communications Biology. 1:226: https://doi.org/10.1038/s42003-018-0236-y. PDF
Srinivasan, B, Tonddast-Navaei S, Roy A, Zhou H, Skolnick J. 2018 Chemical Space of Escherichia coli Dihydrofolate Reductase Inhibitors: New Approaches for Discovering Novel Drugs for Old Bugs. Medicinal Research Reviews. 1-22. PDF
Zhou, H, Gao M, Skolnick J. 2018. ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations. PlosOne. 13(5):e0196849. PDF
Snell, T, Johnson R, Matthews AB, Zhou H, Gao M, Skolnick J. 2018. Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers. Biogerontology. PDF
Skolnick, J, Zhou H. 2017. Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods? The Journal of Physical Chemistry B. 121(15):3546-3554. PDF
Skolnick, J, Gao M, Zhou H. 2016. How special is the biochemical function of native proteins? F1000Research. 5:207. PDF
Zhou, H, Gao M, Skolnick J. 2016. ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures. PLOS ONE. 11(3):e0150965. PDF
Zhou, H, Skolnick J. 2016. A knowledge-based approach for predicting gene-disease associations. Bioinformatics. 32(18): 2831-8. PDF
Srinivasan, B, Zhou H, Mitra S, Skolnick J. 2016. Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway. Bioorganic & Medicinal Chemistry. 24(19):4750-4758. PDF
Snell, TW, Johnston RK, Srinivasan B, Zhou H, Gao M, Skolnick J. 2016. Repurposing FDA-approved drugs for anti-aging therapies. Biogerontology. 17(5-6):907-920. PDF
Skolnick, J, Gao M, Roy A, Srinivasan B, Zhou H. 2015. Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorganic & Medicinal Chemistry Letters. 25:1163-1170. PDF
Zhou, H, Gao M, Skolnick J. 2015. Comprehensive prediction of drug-protein interactions and side effects for the human proteome. Scientific Reports. 5:11090. PDF
Gao, M, Zhou H, Skolnick J. 2015. Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. Structure. 23(7):1362-1369. PDF
Boles, RG, Hornung HA, Moody AE, Ortiz TB, Wong SA, Eggington JM, Stanley CM, Gao M, Zhou H, McLaughlin S et al.. 2015. 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. Mitochondrion. 23:64-70. PDF
Khoury, GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y et al.. 2014. WeFold: A Coopetition for Protein Structure Prediction. Proteins: Structure, Function, and Bioinformatics. 82(9): 1850-68. PDF
Srinivasan, B, Zhou H, Kubanek J, Skolnick J. 2014. Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. Journal of Cheminformatics. 6(1):16. PDF
Kufareva, I, Katritch V, Stevens R C., Abagyan R, Skolnick J, Zhou H, Roy A. 2014. Advances in GPCR Modeling Evaluated by the GPCR Dock 2013 Assessment: Meeting New Challenges. Structure. 22(8):1120-1139. PDF
Skolnick, J, Gao M, Zhou H. 2014. On the Role of Physics and Evolution in Dictating Protein Structure and Function. Israel Journal of Chemistry. 54(8-9):1176-1188. PDF
Zhou, H, Skolnick J. 2013. FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. Journal of Chemical Information and Modeling. 53(1):230-240. PDF
Skolnick, J, Zhou H, Gao M. 2013. Are predicted protein structures of any value for binding site prediction and virtual ligand screening? Current opinion in structural biology. 23(2):191-7. PDF
Zhou, H, Skolnick J. 2012. Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF
Zhou, H, Skolnick J. 2012. FINDSITEX: A Structure-Based, Small Molecule Virtual Screening Approach with Application to All Identified Human GPCRs. Molecular Pharmaceutics. 9(6):1775-1784. PDF
Skolnick, J, Zhou H, Brylinski M. 2012. Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures. The Journal of Physical Chemistry B. 116(23):6654-6664. PDF