Jie Liang

Personal Home Page

http://www.uic.edu/depts/bioe/faculty/j_liang/index.htm

Articles in Scholarly Journals [Incomplete List]

  1. Foreword
    Algorithmica, vol. 48, no. 4, pp. 301–301, 2007
  2. Predicting Enzyme Functional Surfaces and Locating Key Residues Automatically from Structures
    Annals of Biomedical Engineering, vol. 35, no. 6, pp. 1037–1042, 2007
  3. Sequence Motifs and Antimotifs in ß-Barrel Membrane Proteins from a Genome-Wide Analysis: The Ala-Tyr Dichotomy and Chaperone Binding Motifs
    Journal of Molecular Biology, vol. 363, no. 2, pp. 611–623, 2006
  4. Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors
    Proteins: Structure, Function, and Bioinformatics, vol. 63, no. 4, pp. 949–960, 2006
  5. Prediction of buried helices in multispan alpha helical membrane proteins
    Proteins: Structure, Function, and Bioinformatics, vol. 63, no. 1, pp. 1–5, 2006
  6. Monte Carlo sampling of near-native structures of proteins with applications
    Proteins: Structure, Function, and Bioinformatics, vol. 66, no. 1, pp. 61–68, 2006
  7. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Nucleic Acids Research, vol. 34, no. Web Server, pp. W116–W118, 2006
  8. Protein Folding Dynamics via Quantification of Kinematic Energy Landscape
    Physical Review Letters, vol. 96, no. 5, 2006
  9. BMC Structural Biology, vol. 6, no. 1, p. 13, 2006
  10. Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions†
    Photochemistry and Photobiology, vol. 82, no. 6, p. 1426, 2006
  11. Protein surface analysis for function annotation in high-throughput structural genomics pipeline
    Protein Science, vol. 14, no. 12, pp. 2972–2981, 2005
  12. The membrane–water interface region of membrane proteins: structural bias and the anti-snorkeling effect
    Trends in Biochemical Sciences, vol. 30, no. 7, pp. 355–357, 2005
  13. Geometric cooperativity and anticooperativity of three-body interactions in native proteins
    Proteins: Structure, Function, and Bioinformatics, vol. 60, no. 1, pp. 46–65, 2005
  14. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins
    Proteins: Structure, Function, and Bioinformatics, vol. 59, no. 3, pp. 496–509, 2005
  15. Interstrand Pairing Patterns in ß-Barrel Membrane Proteins: The Positive-outside Rule, Aromatic Rescue, and Strand Registration Prediction
    Journal of Molecular Biology, vol. 354, no. 4, pp. 979–993, 2005
  16. Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach
    Molecular Biology and Evolution, vol. 23, no. 2, pp. 421–436, 2005
  17. Developing optimal non-linear scoring function for protein design
    Bioinformatics, vol. 20, no. 17, pp. 3080–3098, 2004
  18. pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
    Nucleic Acids Research, vol. 32, no. Web Server, pp. W555–W558, 2004
  19. Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models
    The Journal of Chemical Physics, vol. 121, no. 1, p. 592, 2004
  20. Are Residues in a Protein Folding Nucleus Evolutionarily Conserved?
    Journal of Molecular Biology, vol. 335, no. 4, pp. 869–880, 2004
  21. Protein?Protein Interactions: Hot Spots and Structurally Conserved Residues often Locate in Complemented Pockets that Pre-organized in the Unbound States: Implications for Docking
    Journal of Molecular Biology, vol. 344, no. 3, pp. 781–795, 2004
  22. The DNA Architectural Protein HMGB1 Facilitates RTA-Mediated Viral Gene Expression in Gamma-2 Herpesviruses
    Journal of Virology, vol. 78, no. 23, pp. 12940–12950, 2004
  23. Membrane-Associated and Secreted Genes in Breast Cancer
    Cancer Research, vol. 64, no. 23, pp. 8682–8687, 2004
  24. Interhelical Hydrogen Bonds in Transmembrane Region Are Important for Function and Stability of Ca2+-Transporting ATPase
    Cell Biochemistry and Biophysics, vol. 39, no. 1, pp. 1–12, 2003
  25. Higher-order Interhelical Spatial Interactions in Membrane Proteins
    Journal of Molecular Biology, vol. 327, no. 1, pp. 251–272, 2003
  26. Structural Location of Disease-associated Single-nucleotide Polymorphisms
    Journal of Molecular Biology, vol. 327, no. 5, pp. 1021–1030, 2003
  27. Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns
    Journal of Molecular Biology, vol. 332, no. 2, pp. 505–526, 2003
  28. Simplicial edge representation of protein structures and alpha contact potential with confidence measure
    Proteins: Structure, Function, and Genetics, vol. 53, no. 4, pp. 792–805, 2003
  29. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers
    The Journal of Chemical Physics, vol. 118, no. 13, p. 6102, 2003
  30. CASTp: Computed Atlas of Surface Topography of proteins
    Nucleic Acids Research, vol. 31, no. 13, pp. 3352–3355, 2003
  31. Biochemistry, vol. 42, no. 21, pp. 6400–6407, 2003
  32. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method
    The Journal of Chemical Physics, vol. 117, no. 7, p. 3511, 2002
  33. Experimental and computational studies of determinants of membrane-protein folding
    Current Opinion in Chemical Biology, vol. 6, no. 6, pp. 878–884, 2002
  34. Computational analysis of microarray gene expression profiles: clustering, classification, and beyond
    Chemometrics and Intelligent Laboratory Systems, vol. 62, no. 2, pp. 199–216, 2002
  35. Interhelical hydrogen bonds and spatial motifs in membrane proteins: Polar clamps and serine zippers
    Proteins: Structure, Function, and Genetics, vol. 47, no. 2, pp. 209–218, 2002
  36. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins1
    Journal of Molecular Biology, vol. 311, no. 4, pp. 891–907, 2001
  37. Regulation of Glycosaminoglycan Function by Osmotic Potentials. MEASUREMENT OF WATER TRANSFER DURING ANTITHROMBIN ACTIVATION BY HEPARIN
    Journal of Biological Chemistry, vol. 276, no. 52, pp. 49275–49282, 2001
  38. Highly abundant genes in the transcriptosome of human and baboon CD34 antigen-positive bone marrow cells
    Blood, vol. 98, no. 1, pp. 93–99, 2001
  39. Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts
    Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, vol. 1453, no. 2, pp. 239–253, 1999
  40. Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape
    Proteins: Structure, Function, and Genetics, vol. 33, no. 1, pp. 1–17, 1998
  41. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins
    Proteins: Structure, Function, and Genetics, vol. 33, no. 1, pp. 18–29, 1998
  42. On the definition and the construction of pockets in macromolecules
    Discrete Applied Mathematics, vol. 88, no. 1-3, pp. 83–102, 1998
  43. Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II
    Proceedings of the National Academy of Sciences, vol. 94, no. 26, pp. 14406–14411, 1997