Georgia Institute of TechnologyCSSB
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Dr. Hongyi Zhou

Research Scientist II

Center for the Study of Systems Biology

member
Dr. Hongyi Zhou

    Contact information:
  • Center for the Study of Systems Biology
  • 250 14th Street NW
  • GCATT, Room 142
  • Atlanta, GA 30318, Mail Code: 0590
  • Tel: 404-407-8978
  • Fax: 404-385-7478
  • Email:

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.

List of Publications

[1] Hongyi Zhou and Yu-Ping Kuang , ``Coupled-channel effects in hadronic transitions in heavy quarkonium systems', Phys. Rev. D 44, 756-769 (1991).
[2] Hongyi Zhou and Yu-Ping Kuang , ``Difficulties of detecting the intermediate-mass Higgs boson in the associate production channel Phys. Rev. D 47, R3680-3684 (1993).
[3] Hongyi Zhou and Yu-Ping Kuang , ``Detecting the intermediate-mass Higgs boson through the associate production channel Phys. Rev. D 53, 4095-4098 (1996).
[4] Hua Wang, Chong-Sheng Li, Hongyi Zhou and Yu-Ping Kuang, ``Supersymmetric QCD corrections to top quark pair production in photon-photon collision', Phys. Rev. D 54, 4374-4379 (1996).
[5] Chong-Sheng Li, Hongyi Zhou , Yun-Lun Zhu and Jin-Min Yang , ``Strong supersymmetric quantum effects on top quark production at the Fermilab Tevatron', Phys. Lett. B 379 , 135-140 (1996).
[6] Chong-Sheng Li, Jin-Min Yang, Yun-Lun Zhu and Hongyi Zhou, ``Yukawa corrections to top pair production in photon-photon collision', Phys.Rev. D 54, 4662-4676 (1996).
[7] Hongyi Zhou , Chong-Sheng Li and Yu-Ping Kuang , ``Yukawa corrections to top quark production at LHC in Two-Higgs-Doublet models', Phys. Rev. D 55, 4412-4420 (1997).
[8] Chong-Xing Yue, Hongyi Zhou, Yu-Ping Kuang, and Gong-Ru Lu, production rates at the Tevatron and the LHC in topcolor-assisted multiscale Technicolor models', Phys. Rev. D 55, 5541-5548 (1997).
[9] Hongyi Zhou and Chong-Sheng Li, ``Supersymmetric QCD corrections to top quark pair production at LHC', Phys. Rev. D 55, 4421-4429 (1997).
[10] Chong-Sheng Li, Robert J. Oakes, Jin-Min Yang, Hongyi Zhou, `` Supersymmetric QCD corrections to single top quark production at the Fermilab Tevatron' , Phys. Rev. D 57, 2009-2012 (1998).
[11] Hongyi Zhou, Yu-Ping Kuang, Chong-Xing Yue, Hua Wang, Gong-Ru Lu, ``Testing Technicolor models in top quark pair production at high energy photon colliders', Phys. Rev. D 57, 4205-4218 (1998).
[12] Chong-Sheng Li, C.P. Yuan, Hongyi Zhou, ``Supersymmetric QCD parity nonconservation in top quark pairs at the Fermilab Tevatron', Phys. Lett. 424, 76-84 (1998).
[13] Chong-Sheng Li, P. Nadolsky, C.P. Yuan, Hongyi Zhou, ``Signatures of the light gluino in the top quark production', Phys. Rev. D 58, 095004 (1998).
[14] Hongyi Zhou, ``CP violation in top quark pair production at hadron colliders', Phys. Rev. D 58, 114002 (1998).
[15] Hongyi Zhou and Chong-Sheng Li, ``Supersymmetric electroweak corrections to top quark' Commun. Theor. Phys. 30, 465 (1998).
[16] Hongyi Zhou, ``Determining top quark CP violating couplings from', Phys. Lett. B 439, 393-397 (1998).
[17] Xue-Lei Wang, Yu-Ping Kuang, Hongyi Zhou, Hua Wang,Ling Zhang, ``Single top quark production in $e\gamma$ collisions and testing Technicolor models', Phys. Rev. D 60, 014002 (1999).
[18] Hongyi Zhou, Yu-Ping Kuang , Chong-Xing Yue , Hua Wang , Gong-Ru Lu, `` Testing Technicolor models via top quark pair production in high-energy photon collisions', Nucl. Phys. Proc. Suppl. 75 B, 302-304 (1999).
[19] Ling Zhang, Xue-Lei Wang, Yu-Ping Kuang, Hongyi Zhou, ``Pseudogoldstone boson effects in top - anti -top productions at high-energy hadron colliders and testing Technicolor models', Phys. Rev. D 61, 115007 (2000).
[20] Hongyi Zhou, Emad Tajkhorshid, Thomas Frauenheim, and Sandor Suhai, Marcus Elstner, ``Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules', Chem. Phys. 277, 91-103 (2002).
[21] Hongyi Zhou and Yaoqi Zhou, ``Folding rate prediction using total contact distance.', Biophys. J. 82, 458--463 (2002).
[22] Hongyi Zhou and Yaoqi Zhou, ``Stability scale and atomic solvation parameters extracted from 1023 mutation experiments', Proteins, 49, 483-492 (2002).
[23] Apichart Linhananta$^*$, Hongyi Zhou$^*$ and Yaoqi Zhou, ``The dual role of a loop with low loop contact distance in folding and domain swapping', Protein Science, 11, 1695-1701 (2002). [$^*$ equal contribution]
[24] Hongyi Zhou and Yaoqi Zhou, ``Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction', Protein Science 11, 2714-2726 (2002).
[25] Yaoqi Zhou, Hongyi Zhou and Martin Karplus, ``Cooperativity in {\it Scapharca} dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water', J. Mol. Biol., 326, 593-606 (2003) .
[26] Hongyi Zhou and Yaoqi Zhou, ``Predicting the topology of transmembrane helical proteins using mean burial propensity and a Hidden-Markov-Model-based method', Protein Science 12, 1547-1555 (2003)
[27] Hongyi Zhou and Yaoqi Zhou, ``Quantifying the effect of burial of amino acid residues on protein stability', Proteins 54, 315-322 (2004).
[28] Hongyi Zhou and Yaoqi Zhou, `` Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition', Proteins 55, 1005-1013 (2004) .
[29] S. Liu, C. Zhang, H. Zhou, and Y. Zhou, ``A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.', Proteins 56, 93-101 (2004).
[30] C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state.', Protein Science 13, 400-411 (2004).
[31] C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``The dependence of all-atom statistical potentials on training structural database.', Biophys. J. 86, 3349-3358 (2004).
[32] Y. Bai, H. Zhou, and Y. Zhou, ``Critical nucleation size in the folding of small apparently two-state proteins.', Protein Science 13, 1173-1181 (2004).
[33] Hongyi Zhou and Yaoqi Zhou, ``Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments', Proteins. 58, 321-328 (2005).
[34] Hongyi Zhou, C. Zhang, S. Liu, and Y. Zhou, ``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', Nucl. Acids Res., (Server issue) 33, W193--W197 (2005).
[35] Hongyi Zhou and Yaoqi Zhou, ``SPARKS 2 and SP$^3$ servers in CASP 6.', Proteins (Supplement CASP issue), Suppl 7 152--156 (2005).
[36] Hongyi Zhou and Yaoqi Zhou, ``SPEM: Sequence, secondary structure profiles enhanced multiple sequence alignment', Bioinformatics 21, 3615--3621 ( 2005).
[37] Z. Zhou, H. Feng, H. Zhou, Y. Zhou and Y. Bai, ``Design and folding of a multi-domain protein', Biochemistry 44, 12107--12112 (2005).
[38] Y. Zhou, H. Zhou, C. Zhang and S. Liu, ``What is a desirable statistical energy function for proteins and how can it be obtained?', Cell Biochem. Biophys. in press (2006) [Review].