Hongyi Zhou

Research Scientist II

Ph.D., Tsinghua University, 1993

Center for the Study of Systems Biology
250 14th Street, NW, Room 142
Atlanta GA, 30318, Mail Code:0590
Tel :(404) 407-8978
Fax :(404) 385-7478
hzhou3@mail.gatech.edu


Research Interests
Computational Biophysics and Bioinformatics:

  • Development of tools for 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.  FINDSITEX: A structure based, small molecule virtual screening approach with application to all identified human GPCRs. Molecular Pharmaceutics .
Zhou, H, Gao M, Kumar N, Skolnick J.  Submitted.  SUNPRO: Structure and function predictions of proteins from representative organisms. BMC Bioinformatics.
Skolnick, J, Zhou H, Brylinski M.  In Press.  Further evidence for the likely completeness of the library of solved single domain protein structures. Journal of Physical Chemistry, B. PDF
Zhou, H, Skolnick J.  2012.  Template-based protein structure modeling using TASSERVMT. Proteins: Structure, Function, and Bioinformatics. 80(2):352-361. PDF
Brylinski, M, Lee S Y, Zhou H, Skolnick J.  2011.  The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. Journal of Structural Biology. 173(3):558-569. PDF
Zhou, H, Skolnick J.  2011.  GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction. Biophysical Journal. 101(8):2043-2052. PDF
Pandit, S B, Zhou H, Skolnick J.  2010.  TASSER-based protein structure prediction. Introduction to Protein Structure Prediction: Methods and Algorithms. 14:219-242. PDF
Pandit, S B, Brylinski M, Zhou H, Gao M, Arakaki AK, Skolnick J.  2010.  PSiFR: an integrated resource for prediction of protein structure and function. Bioinformatics (Oxford, England). 26(5):687-8. PDF Abstract
Zhou, H, Skolnick J.  2010.  Improving threading algorithms for remote homology modeling by combining fragment and template comparisons. Proteins. 78(9):2041-8. PDF Abstract
Zhou, H, Pandit S B, Skolnick J.  2009.  Performance of the Pro-sp3-TASSER server in CASP8. Proteins. 77 Suppl 9:123-7. PDF Abstract
Zhou, H, Skolnick J.  2009.  Protein structure prediction by pro-Sp3-TASSER. Biophysical journal. 96(6):2119-27. PDF Abstract
Zhou, H, Skolnick J.  2008.  Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential. Proteins. 71(3):1211-8. PDF Abstract
Zhou, H, Skolnick J.  2007.  Ab initio protein structure prediction using chunk-TASSER. Biophysical journal. 93(5):1510-8. PDF Abstract
Zhou, H, Pandit S B, Lee SY, Borreguero J, Chen H, Wroblewska L, Skolnick J.  2007.  Analysis of TASSER-based CASP7 protein structure prediction results. Proteins. 69 Suppl 8:90-7. PDF Abstract
Zhou, H, Xue B, Zhou Y.  2007.  DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile.. Protein science : a publication of the Protein Society. 16(5):947-55. Abstract
Zhou, Y, Zhou H, Zhang C, Liu S.  2006.  What is a desirable statistical energy function for proteins and how can it be obtained? Cell biochemistry and biophysics. 46(2):165-74. Abstract
Zhou, H, Zhou Y.  2005.  Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments.. Proteins. 58(2):321-8. Abstract
Zhou, H, Zhou Y.  2005.  SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.. Bioinformatics (Oxford, England). 21(18):3615-21. Abstract
Zhou, H, Zhou Y.  2005.  SPARKS 2 and SP3 servers in CASP6.. Proteins. 61 Suppl 7:152-6. Abstract
Zhou, H, Zhang C, Liu S, Zhou Y.  2005.  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.. Nucleic acids research. 33(Web Server issue):W193-7. Abstract
Zhou, Z, Feng H, Zhou H, Zhou Y, Bai Y.  2005.  Design and folding of a multidomain protein.. Biochemistry. 44(36):12107-12. Abstract
Zhou, H, Zhou Y.  2004.  Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition.. Proteins. 55(4):1005-13. Abstract
Zhang, C, Liu S, Zhou H, Zhou Y.  2004.  An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state.. Protein science : a publication of the Protein Society. 13(2):400-11. Abstract
Liu, S, Zhang C, Zhou H, Zhou Y.  2004.  A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.. Proteins. 56(1):93-101. Abstract
Zhou, H, Zhou Y.  2004.  Quantifying the effect of burial of amino acid residues on protein stability.. Proteins. 54(2):315-22. Abstract
Zhang, C, Liu S, Zhou H, Zhou Y.  2004.  The dependence of all-atom statistical potentials on structural training database.. Biophysical journal. 86(6):3349-58. Abstract
Bai, Y, Zhou H, Zhou Y.  2004.  Critical nucleation size in the folding of small apparently two-state proteins.. Protein science : a publication of the Protein Society. 13(5):1173-81. Abstract
ZHOU, YQ, Zhou H, ZHANG C, et al.  2004.  Toward a physical energy function for intra- and inter-protein interactions by combining structural knowledge with physical principles. BIOPHYSICAL JOURNAL. 86 (1):306A-307A.
Zhou, H, Zhou Y.  2003.  Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method.. Protein science : a publication of the Protein Society. 12(7):1547-55. Abstract
Zhou, Y, Zhou H, Karplus M.  2003.  Cooperativity in Scapharca dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water.. Journal of molecular biology. 326(2):593-606. Abstract
Zhou, H, Zhou Y.  2002.  Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.. Protein science : a publication of the Protein Society. 11(11):2714-26. Abstract
Zhou, H, Zhou Y.  2002.  Folding rate prediction using total contact distance.. Biophysical journal. 82(1 Pt 1):458-63. Abstract
Zhou, H, Zhou Y.  2002.  Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.. Proteins. 49(4):483-92. Abstract
Linhananta, A, Zhou H, Zhou Y.  2002.  The dual role of a loop with low loop contact distance in folding and domain swapping.. Protein science : a publication of the Protein Society. 11(7):1695-701. Abstract
Zhou, H, TAJKHORSHID E, FRAUENHEIM T, et al.  2002.  Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules. CHEMICAL PHYSICS. 277:91-103. PDF
Zhou, H, ZHOU YQ.  2002.  Distance-scaled, finite ideal-gas reference state improves structure- derived potentials of mean force for structure selection and stability prediction. PROTEIN SCIENCE. 12 (9):2121-21.
WANG, XL, KUANG YP, Zhou H, et al.  1999.  Single top quark production in e gamma collisions and testing technicolor models. PHYSICAL REVIEW D. 60 (1) :4002.
Li, CS, OAKES RJ, YANG JM, Zhou H.  1998.  Supersymmetric QCD corrections to single top quark production at the Fermilab tevatron. PHYSICAL REVIEW D. 57:2009-2012.
Zhou, H, KUANG YP, YUE CX, et al.  1998.  Testing technicolor models in top quark pair production at high energy photon colliders. PHYSICAL REVIEW D. 57 ( 7):4205-18.
Zhou, H.  1998.  CP violation in top quark pair production at hadron colliders. PHYSICAL REVIEW D. 58 (11):4002.
Li, CS, YUAN CP, Zhou H.  1998.  Supersymmetric QCD parity nonconservation in top quark pairs at the Tevatron. PHYSICS LETTERS B. 424 (1-2):76-84.
Zhou, H.  1998.  Determining top quark CP violating dipole couplings from e(+)e(-)- >(tt)over-bar. PHYSICS LETTERS B. 439 (3-4):393-397.
YUE, CX, Zhou H, KUANG YP, et al.  1997.  t(t)over-bar production rates at the Fermilab Tevatron and the CERN LHC in top-color-assisted multiscale technicolor models. PHYSICAL REVIEW D. 55:5541-5548.
Zhou, H, Li CS.  1997.  Supersymmetric QCD corrections to top quark pair production at CERN LHC. PHYSICAL REVIEW D. 55 (7):4421-29.
Zhou, H, Li CS, KUANG YP.  1997.  Yukawa corrections to top quark production at the CERN LHC in two-Higgs-doublet models. PHYSICAL REVIEW D . 55 (7):4412-4420.
Li, CS, Zhou H, ZHU YL, et al.  1996.  Strong supersymmetric quantum effects on top quark production at the Fermilab Tevatron. PHYSICS LETTERS B. 379 (1-4):135-140.
Li, CS, YANG JM, ZHU YL, Zhou H.  1996.  Yukawa corrections to top quark pair production in photon-photon collisions. PHYSICAL REVIEW D. 54 (7):4662-4676.
WANG, H, Li CS, Zhou H, et al.  1996.  Supersymmetric QCD corrections to top quark pair production in photon-photon collisions. PHYSICAL REVIEW D. 54 (7):4374-79.
Zhou, H, KUANG YP.  1996.  Detecting the intermediate-mass Higgs boson through the associate production channel pp->t(t)over-bar-HX. PHYSICAL REVIEW D. 53 (7):4095-98.
Zhou, H, KUANG YP.  1993.  DIFFICULTIES OF DETECTING THE INTERMEDIATE-MASS HIGGS-BOSON IN THE ASSOCIATED PRODUCTION CHANNEL PP- ]T(T)OVER-BAR-HX. PHYSICAL REVIEW D. 47 (9):R3680-R3684.
Zhou, H, KUANG YP.  1991.  COUPLED-CHANNEL EFFECTS IN HADRONIC TRANSITIONS IN HEAVY-QUARKONIUM SYSTEMS . PHYSICAL REVIEW D. 44 (3):756-769.

Skolnick Group

Services
PSIFR
Protein Structure Prediction
chunk-TASSER
MetaTASSER
pro-sp3-TASSER
TASSER
Protein Structure Refinement
BSR
Protein Structure Alignment
Fr-TM-align
iAlign
DNA-binding Prediction
DBD-Threader
DBD-Hunter
DP-dock
Protein Function Prediction
FINDSITE
FINDSITE-metal
EFICAz2.5
Ligand Docking/Screening
FINDSITELHM
Q-DockLHM
Software
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EFICAz2.5
FINDSITE
FINDSITELHM
FINDSITE-metal
Fr-TM-align
iAlign
PULCHRA
TASSER-Lite
Databases
Structure Prediction Libraries
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Human GPCRs
E. coli Proteome
PDB-like Structures
Function Prediction Libraries
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KinomeLHM
X-ReactKIN
Human Proteome
Human DNA Binders
Reference Libraries
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Active Site Templates
Apo/Holo Pairs
Simulations
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E. coli Intracellular Dynamics
PSIFR - a web portal that provides access to TASSER, TASSER-Lite and MetaTASSER and DBD-Hunter, and the enzyme function inference engine EFICaz2.
MetaTASSER - a protein structure prediction server that uses three
state-of-the-art threading methods PROSPECTOR_3, SP3 and SPARKS to identify templates that are selected by 3D-Jury. For targets with no reliable templates, chunk models from chunk-TASSER are also included. SPICKER clustering is used to select the final models from the TASSER trajectory. Detailed atomic models are then built using PULCHRA.
pro-sp3-TASSER - uses a single threading method with multiple scoring to identify templates. Short TASSER runs generate full length models that are selected by TASSER-QA and FTCOM ranking procedures. pro-sp3-TASSER performs better than MetaTASSER for medium/hard targets but is computationally more expensive.
Fr-TM-align - structural alignment program for monomeric proteins that uses the TM-score as the structure comparison metric.
iAlign - structural alignment algorithm for protein-protein interfaces that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
DBD-Threader - a server that predicts DNA-binding protein domains from a protein's sequence.
DBD-Hunter - a server that predicts DNA-binding protein domains given a protein’s structure.
DP-dock - a server that predicts the structure of the DNA/protein complex structure given the tertiary structure of a known DNA-binding protein.
FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins. Crystal structures as well as protein models can be used as the target structures.
FINDSITE-metal - a simple extension of FINDSITE that predicts metal-binding sites, residues and binding metal preferences from evolutionarily related templates detected by threading. Furthermore, it employs machine learning to significantly improve the prediction accuracy particularly against modeled protein structures.
FINDSITELHM - a homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.
Q-DockLHM - a low-resolution ligand docking/refinement approach applicable to the modeled structures of target receptors. It uses pocket-specific statistical potentials and harmonic restraints imposed on the binding poses of the common molecule substructures extracted from evolutionarily related proteins.
EFICAz2.5 - an accurate sequence based approach to enzyme function inference.
chunk-TASSER - a protein structure prediction method that combines threading templates from SP3 and ab initio folded chunk structures (three consecutive segments of regular secondary structures).
BSR - Binding Site Refinement employs a new template-based method for the local refinement of ligand-binding regions in protein models using closely as well as distantly related templates identified by threading.
FINDSITE - a threading-based binding site prediction/protein functional inference/ligand screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins.
Fr-TM-align - a program for protein structural alignment that uses the TM-score as the structural comparison metric. This is an improved version of Tm-align.
iAlign - a structural alignment algorithm for the protein-protein interface that uses the TM-score as well as a side-chain contact overlap weighted TM-score as the interface comparison metric.
PULCHRA - a program for all-atom reconstruction from the backbone C-alpha atoms.
TASSER-Lite - a comparative protein structure modeling tool.
Human GPCRs - Predicted structures of 907 G protein-coupled receptors in the Human proteome.
Human DNA Binders - DBD-Threader Predictions on the Human proteome. A list of predicted Human DNA-binding proteins their Sequences and predicted 3D models.
E. coli Poteome - Predicted structures of the E. Coli proteome.
PDB-like Structures - A library of 15,000 compact homopolypeptide structures that cover the PDB.
Active Site Templates - Automated Functional Templates (AFT) for Enzyme Active Site Prediction.
Apo/Holo Pairs - Apo/Holo and Holo/Holo protein pairs. The global structures of apo and holo protein.
KinomeLHM - Comprehensive structural and functional characterization of the human kinome by protein structure predication and ligand virtual screening.
Human Proteome - Structure modeling, function annotation and ligand virtual screening of the human proteome.
TASSER - A meta server for protein structure prediction that combines chunk-TASSER, pro-sp3-TASSER and MetaTASSER.
FINDSITELHM - A homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction.
E. coli Intracellular Dynamics - The inside of cells is highly crowded with bio-macromolecules, such as proteins, DNA, RNA. This environment is quite different from the conditions in a test tube that we usually use for analysis of biomolecular functions, where the macromolecular concentration is ~100 times less than inside cells.
X-ReactKIN - Virtual cross-reactivity profiles of the human kinome.