Dr. Huiling Chen

Computational Systems Biology laboratory (CSBL)
Department of Biochemistry & Molecular Biology &
Institute of Bioinformatics
The University of Georgia

Phone: (706)542-9762
Fax: (706)542-9751
E-mail:

I will join Pfizer Inc in Mar 2011 and may no longer update this page.
You can still reach me by the above email.

Research Interests:

I am generally interested in developing computational methods for modeling protein structures and interactions, and applying these tools to solve biological problems. My past and ongoing projects include:
  • High-resolution protein tertiary structure prediction
  • Transmembrane protein structure prediction
  • Protein-protein interaction & quaternary structure prediction
  • Protein-ligand docking

Current Research:

  • Method development

    1. Membrane protein structure prediction
      Membrane protein structures are difficult to determine by both experimental techniques and de novo structure prediction methods. Collaborting with NMR experimentalists and computational physicists, we are developing hybrid methods by a combined use of limited experimental data constraints and Wang-Landau Monte Carlo simulation.
      Our collaborators: Dr. James Prestegard's group at CCRC, Dr. David Landau's group at CSP

    2. Protein threading/fold recognition
      Current PDB is esstentially complete for the (soluble) protein structure prediction problem, yet most of the structure templates are not detectable by current threading method. Although side-chain interactions are important information for structure prediction, incorporating the information in threading is NP-hard problem. To substantially improve the state-of-the-art of protein threading, we have been developing a novel threading framework that considers backbone threading and side-chain packing simultaneously in a generalized threading paradigm.
      Our collaborators: Dr. Yang Zhang's group at Umich, Dr. Jun Liu's group at Harvard

            Our projects are currently supported by NIH and NSF funding.

  • Application of structure prediction in biological problems

    • In addition to work with the Biofuel, Comparative Genomics and Cancer groups at CSBL, we have been collaborating with experimental biologists in the following areas:

    1. Protein function characterization based on predicted structure
    2. Distant homolog search using structure information
    3. Protein-ligand docking and binding free energy calculation

    Our collaborators include Dr. Debra Mohnen, Dr. Michael Hahn at CCRC,UGA, Dr. CJ Tsai at Genetics,UGA.

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Education:

2005 Ph.D. in Computational Biophysics, Dept. of Physics, Drexel University, Philadelphia
Dissertation: Prediction of Protein Structures and Protein-Protein interactions, a Bioinformatics Approach.
Advisor: Dr. Huan-Xiang Zhou
1996 B.S. in Physical Electronics, Dept. of Materials Science, Fudan University, Shanghai, China

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Work Experience:

3/2011 - Senior Scientist, Vaccine Research, Pfizer Inc.
2008 - 2/2011 Postdoc Research Associate / Group Leader, Structural Bioinformatics Group, Computational Systems Biology Lab, University of Georgia (with Dr. Ying Xu )
2005 - 2007 Postdoctoral Fellow, Center for the Study of Systems Biology, Georgia Institute of Technology (with Dr. Jeffrey Skolnick, lab moved from New York State Center of Excellence in Bioinformatics & Life Sciences in 2006)
1999 - 2005 Research/Teaching Assistant, Dept. of Physics, Drexel University
1996 - 1998 Technical Support Engineer / Sales / Account Manager, Shanghai Fudan Kingstar Computer Co.,Ltd. (now Sungard China)

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Awards & Honors:

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Publications:

Y. Ou*, H. Chen*, G. Li, F. Ji, S. Wu, Y. Zhang, Y. Xu. "SCITRED: a novel protein threading algorithm that considers backbone threading and side-chain packing simultaneously." (* equal contribution) to be submitted
H. Chen, F. Ji, V. Olman, C.K. Mobley, Y. Liu, Y. Zhou, J.H. Bushweller, J.H. Prestegard, Y. Xu (2011). "Optimal mutation sites for PRE data collection and membrane protein structure prediction." Structure, 19:484-495. [Commentary]
Y. Yin, H. Chen, M. Hahn, D. Mohnen, Y. Xu (2010). "Evolution and function of the plant cell wall synthesis-related Glycosyltransferase Family 8." Plant Physiology, 153:1729-46.
F. Zhou, H. Chen, Y. Xu (2010). "GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems." BMC Microbiology, 10:69. [Website]
F. Mao, Y. Yin, F. Zhou, W. Chou, C. Zhou, H. Chen, Y. Xu (2009). "pDAWG: an integrated database for plant cell-wall genes." BioEnergy Research, 2:209–216. [Website]
H. Chen and J. Skolnick (2008). "M-TASSER: An Algorithm for Protein Quaternary Structure Prediction." Biophysical Journal, 94:918-928. [Citations]
H. Zhou, S. B. Pandit, S. Lee, J. Borreguerro, H. Chen, L. Wroblewska and J. Skolnick (2007). "Analysis of TASSER based CASP7 protein structure prediction results." Proteins, 69 Suppl 8:90-97. ( invited paper for CASP. Citations )
H. Chen and H.-X. Zhou (2005). "Prediction of solvent accessibility and sites of deleterious mutation from protein sequences." Nucl. Acids Res., 33: 3193-3199. [Server] [Download] [Citations]
( An expanded version for real-value solvent accessibility predictoin is available here. The program is incorporated in the No.1 protein structure prediction server I-TASSER)
A. D. J. van Dijk , S. J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou, and A. M. J. J. Bonvin (2005). "Data-driven docking: HADDOCK's adventures in CAPRI." Proteins, 60:232-238. ( invited paper for CAPRI. Citations )
H. Chen and H.-X. Zhou (2005). "Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data." Proteins, 61:21-35. [Server] [Citations]
H. Chen, H.-X. Zhou, X. Hu and I. Yoo (2004). "Classification Comparison of Prediction of Solvent Accessibility From Protein Sequences." Proceedings of the Second Asia-Pacific Bioinformatics Conference, 29: 333-338.

Conference presentations:

Y. Yin, H. Chen, B. Cantwell, I. Jouline, M. Hahn, D. Mohnen, Y. Xu. "The plant cell wall biosynthesis related Galacturonosyltransferase (GAUT) and GAUT like (GATL) genes have a different origin than the other Glycosyltransferase family 8 genes." Genomics:GTL Awardee Workshop VII, Bethesda, Maryland, February 8-11, 2009.
F. Mao, F. Zhou, W. Chou, Y. Yin, H. Chen, C. Zhou, Y. Xu. "pDAWG: plant Database of Annotated cell Wall Genome." BioEnergy Science Center 2nd retreat, Chattanooga, TN, December 1-3, 2008.
Y. Yin, H. Chen, B. Cantwell, I. Jouline, M. Hahn, D. Mohnen, Y. Xu. "Computational study of the plant GT8 genes: insight about their origin and function." BioEnergy Science Center 2nd retreat, Chattanooga, TN, December 1-3, 2008.
H. Zhou, S. Y. Lee, S. Pandit, H. Chen, J. Borreguero and J. Skolnick. "TASSER for protein structure prediction in CASP7." The Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar Conference Center, California, November 26-30, 2006.
S. B. Pandit, H. Zhou, J. Borreguero, S. Lee, H. Chen and J. Skolnick. "MetaTasser: A 3D-jury threading approach with TASSER model assembly/refinement." The Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP7), Asilomar Conference Center, California, November 26-30, 2006.
H. Chen, H.-X. Zhou, X. Hu and I. Yoo. "Classification Comparison of Prediction of Solvent Accessibility From Protein Sequences." The Second Asia-Pacific Bioinformatics Conference , Dunedin, New Zealand, Jan 18-22, 2004.
H. Chen and H-X Zhou. "Prediction of interface residues in protein-protein complexes. Test against NMR data." The Second Conference in Modeling of Protein Interactions in Genomes, Stony Brook, June 27-30, 2003.
H. Chen and H-X Zhou. "Prediction of interface residues in protein-protein complexes." Biophysical Society 47th Annual Meeting, San Antonio, March 1-5, 2003.
H. Chen and H.-X. Zhou. "Improving Fold Recognition and Query-Template Alignment by Combining PSI-Blast and Sequence-Structure Threading." The Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP5), Asilomar Conference Center, California, December 1-5, 2002.
H. Chen and H.-X. Zhou. "Prediction of Solvent Accessibility and Sites of Deleterious Mutations from Protein Sequences." Biophysical Society 46th Annual Meeting, San Francisco, February 23-27, 2002.

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Services:

  • Seminar Coordinator, CSBL,UGA
  • Program Committee Member: The International Bioinformatics Workshop (IBW2009, IBW2010)
  • Reviewer: Proteins, Bioinformatics, Nucleic Acids Research, PLoS Computational Biology, BMC Bioinformatics, BMC Structural Biology, Current Protein & Peptide Science, Mathematical Biosciences, International Journal of Bioinformatics Research and Applications, International Conference on Computational Systems Bioinformatics (CSB2008, CSB2009), Asia Pacific Bioinformatics Conference (APBC2009), International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics 2011), SwissNSF 2009

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Links:

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