2008

Jie Liang, Yan-Yuan Tseng, Joseph Dundas, Andrewn Binkowski, Andrzej Joachimiak, Zheng Ouyang, and Larisa Adamian. Chapter 4: Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces, Advances in protein chemistry. 2008, 75:107-141

Ronald Jackups, Jr and Jie Liang. Combinatorial analysis for sequence and spatial motif discovery in short sequence fragments. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008, Accepted
An appendix describing an alternative positional null model is here. (final version pending)

Ming Lin, Hsiao-Mei Lu, Rong Chen, and Jie Liang. Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints J Chem Phys. 2008, 129(094101):1-13

Youfang Cao, Hsiao-Mei Lu, and Jie Liang. Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda Conf Proc IEEE Eng Med Biol Soc. 2008, 30:611-614

David Jimenez-Morales, Larisa Adamian, and Jie Liang. Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins Conf Proc IEEE Eng Med Biol Soc. 2008, 30:1347-1350

Zheng Ouyang and Jie Liang. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Science, 2008, 17(7):1256-63

Youfang Cao and Jie Liang. Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability BMC Systems Biology, 2008, 2:30:1-13 doi:10.1186/1752-0509-2-30.

Jerry Osagie Ebalunode, Zheng Ouyang, Jie Liang, and Weifan Zheng. A novel approach to structure-based pharmacophore search using computational geometry and shape matching techniques J Chemical Information and Modeling, 2008, 48(4):889-901

Jian Zhang, Ming Lin, Rong Chen, Wei Wang, and Jie Liang. Discrete state model and accurate estimation of loop entropy of RNA secondary structures J Chem Phys. 2008, 128(125107):1-10, DOI:10.1063/1.2895050 Abstract.

Ming Lin, Rong Chen, and Jie Liang. Statistical geometry of lattice chain polymers with voids of defined shapes: Sampling with strong constraints J Chem Phys. 2008, 128(084903):1-12 DOI:10.1063/1.2831905

2007

Joe Dundas, T Andrew Binkowski, Bhaskar DasGupta, and Jie Liang. Topology independent protein structural alignment BMC Bioinformatics, 2007, 8:388, doi:10.1186/1471-2105-8-388

Youfang Cao and Jie Liang. An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules Conf Proc IEEE Eng Med Biol Soc. 2007, 29:4599-4602.

Hsiao-Mei Lu and Jie Liang. Perturbation-based Markovian Transmission Model for Macromolecular Machinery in Cell Conf Proc IEEE Eng Med Biol Soc. 2007, 29:5029-5034.

Zheng Ouyang and Jie Liang. Detecting Positively Selected Sites From Amino Acid Sequences: An Implicit Codon Model Conf Proc IEEE Eng Med Biol Soc. 2007, 29:5302-5306.

Joe Dundas, T.A. Binkowski, Bhaskar DasGupta and Jie Liang. Topology Independent Protein Structural Alignment 7th Workshop on Algorithms in Bioinformatics, R. Giancarlo and S. Hannenhalli (Eds.), 2007, LNBI 4645:171-182

Yan Yuan Tseng and Jie Liang. Predicting enzyme functional surfaces and locating key residues automatically from structures. Annals of Biomedical Engineering, 2007, 35(6):1037-1042

Jinfeng Zhang, Ming Li, Rong Chen, Jie Liang, and Jun Liu. Monte Carlo sampling of near-native structures of proteins with applications. Proteins, 2007, 66(1):61-68.

2006

Larisa Adamian, Zheng Ouyang, Yan Yuan Tseng, Jie Liang. Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions Photochem Photobiol. 2006, 82(6):1426-1435

Ronald Jackups, Jr. Sarah Cheng and Jie Liang. Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs J Mol Biol. 2006, 363(2):611-23.
Data: ( Supplementary data of various propensities are here.)

Larisa Adamian and Jie Liang. Prediction of transmembrane helix orientation in polytopic membrane proteins BMC Structural Biology, 2006, 6(13):1-17, doi:10.1186/1472-6807-6-13

Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz and Jie Liang. CASTp: computer atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Research, 2006, 34:W116-118, doi:10.1093/nar/gkl282

Sema Kachalo, Hsiao-Mei Lu and Jie Liang. Protein folding dynamics via quantification of kinematic energy landscape Physical Review Letters, 2006, 96:058105:1-4.

Xiang Li and Jie Liang. Chapt 3. Knowledge-based energy functions for computational studies of proteins.
Ying Xu, Dong Xu, Jie Liang: Computational Methods for Protein Structure Prediction and Modeling, Volume 1:Basic Characterization, 2006 pg. 71-124. Editor-in-Chief: Elias Greenbaum, © 2007 Springer Science, 233 Spring Street, New York, NY 10013, USA: ISBN 10:0-387-33319-3

Yan-Yuan Tseng and Jie Liang. Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity Conf Proc IEEE Eng Med Biol Soc. 2006, 1:4552-4555.

Jie Liang. Chapt 6. Computation of protein geometry and its applications: Packing and function prediction
Ying Xu, Dong Xu, Jie Liang: Computational Methods for Protein Structure Prediction and Modeling, Volume 1:Basic Characterization, 2006 pg. 181-206. Editor-in-Chief: Elias Greenbaum, © 2007 Springer Science, 233 Spring Street, New York, NY 10013, USA: ISBN 10:0-387-33319-3

Larisa Adamian and Jie Liang. Prediction of buried helices in multispan alpha helical membrane proteins Proteins, 2006, 63:1-5.

Yan Yuan Tseng and Jie Liang. Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: A Bayesian Monte Carlo approach Mol Biol Evo. 2006, 23:421-436.

2005

Ronald Jackups, Jr. and Jie Liang. Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction J Mol Biol. 2005, 354:979-993.
A more useful description of the techniques is in the Supplementary Material .
See also the Editor's Choice of the Science magazine.

Jinfeng Zhang, Rong Chen and Jie Liang. Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors Proteins, 2005, 63(4):949-960.
See data files for supplimentary data and program files for Perl scripts and C++ program source code.

T. Andrew Binkowski, Andrzej Joachimiak, and Jie Liang. Protein surface analysis for function annotation in high-throughput structural genomics pipeline Protein Science, 2005, 14:2972-2981.

Xiang Li, and Jie Liang. Geometric cooperativity and anti-cooperativity of three-body interactions in native proteins. Proteins, 2005, 60:46-65.

Jie Liang, Larisa Adamian, and Ronald Jackups, Jr. The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect. Trends in Biochemical Sciences, 2005, 30(7):355-357.

Larisa Adamian, Vikas Nanda, William F. DeGrado, and Jie Liang. Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins Proteins, 2005, 59:496-509.

Xiang Li, and Jie Liang. Computational design of combinatorial peptide library for modulating protein-protein interactions. Pacific Symposium on Biocomputing, 2005, 28-39.

2004

Xiang Li, Ozlem Keskin, Buyong Ma, Ruth Nussinov and Jie Liang. Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that are pre-organized in the unbound states. Implications to docking J Mol Biol. 2004, 344:781-795

Jeffrey Tseng and Jie Liang. Estimating evolutionary rate of local protein binding surfaces: a Bayesian Monte Carlo approach Conf Proc IEEE Eng Med Biol Soc. 2004, 27:739-742

Sema Kachalo, Hsiao-Mei Lu, and Jie Liang. Protein folding dynamics in lattice model with physical movement Conf Proc IEEE Eng Med Biol Soc. 2004, 27:4449-4452.

Nathan Stitziel, Brenton G. Mar, Jie Liang, and Carol Westbrook. Membrane-associated and secreted genes in breast cancer. Cancer Research, 2004 64:8682-8687.

Jinfeng Zhang, Rong Chen, and Jie Liang. Potential function of simplified protein models for discriminating native proteins from decoys: Combining contact interaction and local sequence-dependent geometry. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2976 - 2979 Vol.4 DOI 10.1109/IEMBS.2004.1403844

T. Andrew Binkowski, Bhaskar DasGupta, and Jie Liang. Order independent structural alignment of circularly permuted proteins. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2781 -2784 Vol.4 DOI 10.1109/IEMBS.2004.1403795

Changyu Hu, Xiang Li, and Jie Liang. Developing optimal nonlinear scoring function for protein design Bioinformatics, 2004, 20(17):3080-3098.

Moon Jung Song, Seungmin Hwang, Wendy Wong, June Round, DeeAnn Martinez-Guzman1, Yaron Turpaz, Jie Liang, Ben Wong, Reid C. Johnson, Michael Carey, and Ren Sun. The DNA architectural protein HMGB1 facilitates RTAmediated viral gene expression in gamma2 herpesviruses. J. Virology. 2004, 78(23):12940-12950.

Jinfeng Zhang, Yu Chen, Rong Chen and Jie Liang. Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models. J. Chem. Phys. 2004, 121:592-603.

T. Andrew Binkowski, Patrick Freeman and Jie Liang. pvSOAR: Detecting similar surface patterns of Pocket and Void Surfaces of Amino Acid Residues on proteins. Nucleic Acid Research, 2004, 32:W555-W558.

Yan Yuan Tseng and Jie Liang. Are residues in a protein folding nucleus evolutionarily conserved? J. Mol. Biol. 2004, 335:869-880.

Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif and Jie Liang. topoSNP: A topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acid Research, 2004, 32:D520-D522.

Changyu Hu, Xiang Li and Jie Liang. Optimal nonlinear scoring function for global fitness landscape of protein design. Conf Proc IEEE Eng Med Biol Soc. 2004, 26:2828-2831 Vol.4 DOI 10.1109/IEMBS.2004.1403807

2003

Sema Kachalo, Zarema Arbieva and Jie Liang. Assessing effect of cross-hybridization on oligonucleotide microarrays. Methods of microarray data analysis III, 2003, CAMDA' 02:185-198. DOI 10.1007/b105346

Xiang Li, Changyu Hu, and Jie Liang. Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins, 2003, 53:792-805.

T. Andrew Binkowski, Larisa Adamian and Jie Liang. Inferring functional relationship of proteins from local sequence and spatial surface patterns. J Mol Biol. 2003, 332:505-526.

T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang. CASTp: computed atlas of surface topography of proteins. Nucleic Acid Research, 2003, 31(13):3352-3355. Abstract

Nathan O. Stitziel, Yan Yuan Tseng, Dimitri Pervouchine, David Goddeau, Simon Kasif, and Jie Liang. Structural location of disease-associated single nucleotide polymorphisms. J Mol Biol. 2003, 327:1021-1030.

J. D. Lear, H. Gratkowski, L. Adamian, J. Liang, and W.F. DeGrado Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry, 2003, 42(21):6400-6407.

Larisa Adamian, and Jie Liang. Interhelical hydrogen bonds in transmembrane region are important for function and stability of Ca2+-transporting ATPase. Cell Biochemistry and Biophysics, 2003, 39:1-12.

Larisa Adamian, Ronald Jackups, Jr, T. Andrew Binkowski, and Jie Liang. Higher order interhelical spatial interactions inmembrane proteins. J Mol Biol. 2003, 327:251-272.

Jinfeng Zhang, Rong Chen, Chao Tang, and Jie Liang. Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers. J Chem Phys. 2003, 118(13):6102-6109. (eprint in arxiv)
Data: (SAWs in pdb format and Z_alpha data are here.)

2002

Jie Liang. Experimental and computational studies of the determinants of membrane protein folding. Current Opinion in Chemical Biology, 2002, 6:878-884

Jie Liang, Jinfeng Zhang and Rong Chen. Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method. J Chem Phys. 2002, 117:3511-3521.

Jie Liang and Sema Kachalo. Computational Analysis of Microarray Gene Expression Profiles Clustering, Classification, and Beyond. Chemometrics and Intelligent Laboratory Systems, 2002, 62:199-216.

Larisa Adamian, and Jie Liang. Interhelical hydrogen bonds and spatial motif in membrane proteins: Polar clamps and serine zippers. Proteins, 2002, 47:209-218

Maria P. McGee, Jie Liang, and J. Luba. Hydration effects of heparin on antithrombin probed by osmotic stress. Biophys J. 2002, 82:1040-1049

M. P. McGee and J. Liang. Factor X, Coagulation. Wiley Encyclopedia of Molecular Medicine, 2002

2001

L. Adamian and J. Liang. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol. 2001, 311:891-907

J. Liang and K.A. Dill. Are proteins well-packed? Biophys J. 2001, 81:751-766

M. P. McGee and J. Liang. Regulation of glycosaminoglycan function by osmotic potentials. Measurement of water transfer during antithrombin activation by heparin. J Biol Chem. 2001, 276:49275-49282

I. Gomes, T. L. Sharma, J. D. Kapp, S. Edassery, N. Fulton, J. Liang, R. Hoffman, and C.A. Westbrook. Highly abundant genes in the transcriptosome of human and baboon CD34 antigen-positive bone marrow cells. Blood, 2001, 98:93-99.

1999

C. Yuan, O. Kuwata, J. Liang, S. Misra, S.P. Balashov, T.G. Ebrey. Chloride binding regulates the Schiff base pK in gecko P521 cone-type visual pigment. Biochemistry, 1999, 38:4649-4654.

M.P. McGee, H. Teuschler and J. Liang. Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts. Biochim Biophys Acta. 1999, 1453:239-253

1998

J. Liang, H. Edelsbrunner, and C. Woodward. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science, 1998, 7:1884-1897

H. Edelsbrunner, M. Facello and J. Liang. On the definition and the construction of pockets in macromolecules. Disc Appl Math. 1998, 88:83-102

J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. Analytical shape computing of macromolecules II: identication and computation of inaccessible cavities inside proteins. Proteins, 1998, 33:18-29

J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. Analytical shape computing of macromolecules I: molecular area and volume through alpha shape. Proteins, 1998, 33:1-17.

J. Liang and M.P. McGee. Mechanisms of coagulation factor Xa inhibition by antithrombin. Correlation between hydration structure and water transfer during reactive loop insertion. Biopys J. 1998, 75:573-582.

M.P. McGee, H. Teuschler, and J. Liang. Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain. Biochemistry, 1998, 330:533-539.

1997

J. Liang and S. Subranmaniam. Computation of molecular electrostatics with boundary element methods. Biophys J. 1997, 73:1830-1841

S. Kim, J. Liang, and B.A. Barry. Chemical complementation identies a proton acceptor for redox-active tyrosine D in photosystem II. Proc Natl Acad Sci. 1997, 94:14406-14411.

J.W. Lewis, J. Liang, T.G. Ebrey, M. Sheves, N. Livnah, O. Kuwata, S. Jager, and D.S. Kliger. Early photolysis intermediates of gecko and bovine articial visual pigments. Biochemistry, 1997, 36:14593-14600

1995

H. Edelsbrunner, M. Facello, P. Fu and J. Liang. Measuring proteins and voids in proteins. Proc 28th Ann Hawaii Intl Conf System Sci. 1995, 5:256-264

T.G. Ebrey and J. Liang. The bleaching of visual pigments. Handbook of organic photochemistry and photobiology, 1995, 1484-1491

J. Lewis, J. Liang, T.G. Ebrey, M. Sheves and D.S. Kliger. Chloride effect on the early photolysis intermediates of a gecko cone-type visual pigment. Biochemistry, 1995, 34:5817-5823

1994

J. Liang, G. Steinberg, N. Livnah, M. Sheves and T.G. Ebrey. The pKa of the protonated Schiff base of gecko cone and octopus visual pigments. Biophys J. 1994, 67:848-854.

1993

J. Liang, R. Govindjee, and T.G. Ebrey. Metarhodopsin intermediates of the gecko cone pigment P521. Biochemistry, 1993, 32(51):14187-14193

1987

W. Lin, C. Ma, Z. Luo, W. Fan, Y. Chen and J. Liang. Study on the radiosensitization of AT1727 on human lung adenocarcinoma cell line SPC-A-1. J Rad Res Rad Pro. 1987, 5:58-62.