Jenn-Kang Hwang

黃鎮剛計算生物學教授國立交通大學生物資訊研究所

Jenn-Kang Hwang, Professor of Computational Biology
Institute of Bioinformatics
National Chiao Tung University
HsinChu, Taiwan

One generation passeth away, and another generation cometh: but the earth abideth for ever. Ecc 1: 4

Bioinformatics Center

Bio-computational Lab

Publications

Lin et al. Deriving protein dynamical properties from weighted protein contact number, Proteins: Structure, Function and Bioinformatics [Accepted]
Lu et al. On the relationship between the protein structure and protein dynamics, Proteins: Structure, Function and Bioinformatics [Accepted]
Shih CH, Huang SW, Yen SC, Lai YL, Yu SH, Hwang JK. Computation of protein dynamics without a mechanical model, Proteins: Structure, Function and Bioinformatics (2007) 68, 34-38
Chiu, YY, Hwang JK, Yang JM, Soft energy function and generic evolutionary method for discriminating native from non-native protein conformations, J. Comp. Chem. [Accepted]
Tsai YC, Lin YM, Hwang JK, Yu JSK, On the Stereochemistry of Zn-Zn Bonds: Synthesis, Structural Transformation, and Computations, Chem. Comm. (2007) 40:4125-4127
Su ECY, Chiu HS, Lo A, Hwang JK, TY Sung, WL Hsu, Protein subcellular localization prediction based on compartment-specific features and structure conservation, BMC Bioinformatics (2007) 8:330-341.
Lai YL, Yen SC, Yu SH, Hwang JK. pKNOT: the Protein KNOT web server, Nucleic Acids Research (2007) 35:W420-W424 ; [Go to: The pKNOT server].
Wong YH, Lee TY, Liang HK, Huang CM, Yang YH, Chu CH, Huang HD, Ko MT, Hwang JK, KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns, Nucleic Acids Research (2007) 35:W588-594.
Huang CL, Liu JH, Chiu WC, Huang SW, Hwang JK, Wang WC. Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. J. Biol. Chem. (2007) 282:12220-12229.
Lin YS, Hsu WL, Hwang JK, Li WH. Proportion of solvent-exposed amino acids in a protein and rate of protein evolution, Molecular Biology and Evolution (2007) 24, 1005-11.
Lu CH, Chen YC, Yu CS, Hwang JK. Predicting disulfide connectivity patterns, Proteins: Structure, Function and Bioinformatics (2007) 67: 262-270
Tsai YC, Lin YM, Yu, JSK, Hwang JK. A three-coordinate and quaruply bonded Mo-Mo-Complex, J. Am. Chem. Soc. (2006) 128:13980-13981
Lin YS, Byrnes JK, Hwang JK, Li WH. Codon usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc. Natl. Acad. Sci. USA. (2006) 103:14412-14416
Lin YS, Hwang JK, Li WH. Protein complexity, gene duplicability and gene dispensability in the yeast genome. Gene. (2006) 387, 109-117.
Yu CH, Chen YC, Lu CH, Hwang JK. Prediction of protein subcellular localization. Proteins: Sturcture, Function and Bioinformatics (2006), 64, 643-651
Chiu WC, You JY, Liu JS, Hsu SK, Hsu WH, Shih CH, Hwang JK, Wang WC, Structure-stability-activity relationship in covalently c 1 ross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J. Mol. Biol. (2006), 359: 741-753.
Chen CC, Hwang JK, JM Yang. Protein structure prediction server. Nucleic Acid Research (2006), 34: W152-157. [Go to: (PS)2 server]
Lu CH, Lin SH, Chen YC, Yu CS, Chang SY, Hwang JK. The fragment transformation method to detect the protein structural motifs. Proteins: Sturcture, Function and Bioinformatics (2006), 63:636-643.
Hung SW, Hwang JK, Tseng F, Chang JM Chen CC, Chieng CC. Molecular dynamics simulation on enhancement of CTX and E6 protein binding on mixed SAMs molecules. Nanotechnology (2006), 17, S8-13
Chen YC, Hwang JK Prediction of disulfide connectivity from protein sequences. Proteins: Structure, Function and Bioinformatics (2005) 61, 507-512 .
Huang SW, Hwang JK. Computation of conformational entropy from protein sequences using the machine-learning method – Application to the study of the relationship between structural conservation and local structural stability. Proteins: Structure, Function and Bioinformatics (2005), 59, 802-809.
Liang HK, Huang CM, Ko MT, Hwang JK. The Amino Acid-Coupling Patterns in Thermophilic Proteins. Proteins: Structure, Function and Bioinformatics (2005), 59, 58-63.
Lin YS, Tzeng CS, Hwang JK. Reassessment of morphological characters in freshwater eels (genus Anguilla, Anguillidae) shows congruence with molecular phylogeny estimate. Zoologica Scripta (2005), 34, 225-234.
Chan CC, Liang HK, Hsiao NW, Ko MT, Lyu PC, Hwang JK. The relationship between local structural entropy and protein thermostability. Proteins: Structure, Function and Bioinformatics (2004) 57, 684-691.
Chen YC, Lin YS, Lin CJ and Hwang JK. Prediction of the Bonding States of Cysteines using the Support Vector Machines Based on Multiple Feature Vectors and Cysteine State Sequences. Proteins: Structure, Function and Bioinformatics (2004), 55, 1046-42.
Yu CS, Lin CJ, Hwang JK, Predicting Subcellular Localization of Proteins For Gram-Negative Bacteria by Support Vector Machines Based on n-Peptide Compositions. Protein Science (2004), 13, 1402-1406
Yu JSK, Hwang JK, Tang CY, Yu CH. Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux System with new architectures, updated compilers and library. J. Chem. Inf. Comput. Sci (2004), 44, 635-642.
Yu CS, Wang JY, Yang JM, Lyu PC, Lin CJ, Hwang JK, Fine-grained protein fold assignment by support vector machines using generalized n-peptide coding schemes and jury voting from multiple parameter sets. Proteins: Structure, Function and Genetics. (2003) 50, 531-536.
C-C. Chuang, C-Y Chen, J.-M. Yang, P.-C. Lyu, J.-K. Hwang, Relationship between protein structures and disulfide-bonding patterns. Proteins: Structure, Function and Genetics (2003), 53, 1-5.
J.-T. Horng, H.-D. Huang, S.-H. Wang, M.-Y. Chen, and J.-K. Hwang, Computing motif correlations in proteins. J. Comp. Chem. (2003), 24, 2032-2043.
C. C. Chan, P. C. Lyu, J.-K. Hwang, Computation of the Protein Structure Entropy and its Applications to Protein Folding Processes. J. Chin. Chem. Soc. (2003), 50, 677-684.
J.-M. Yang, C.-H. Tsai, M.-J. Hwang, H.-K. Tsai, J.-K. Hwang, C.-Y. Kao, GEM: A Gaussian evolutionary method for predicting protein side-chain conformations. Protein Sci. (2002), 11, 1897-1907.
J.-K. Hwang, The Partial Averaging Fourier path integral approach based on the harmonic reference path. Theo. Chem. Acc.101 , 359-363 (1999)
Z. Z. Fan, J.-K. Hwang, A. Warshel: Using simplified protein representation as a reference potential for all-atom calculations of folding free energy Theor Chem Acc 103 (1999) 1, 77-80
C.H. Lin, F.C.H. Chan, J.K. Hwang and P.C. Lyu, Calcium binding mode of -carboxyglutamic acids in conantokins Protein Engineering 12, 589-595, (1999)
J.-K. Hwang, Calculation of Quantum Mechanical free energy at low temperature. Theo. Chem. Acc. 98, 202-205 (1998).
A. A. Vyas, J.-J. Pan, H. V. Patel, K. A. Vyas, C.-M. Chiang, Y.-C. Sheu, J.-K. Hwang, W.-g. Wu, Analysis of binding of cobra cardiotoxins to heparin reveals a new beta-sheet heparin-binding structural motif. J. Biol. Chem. 272, 9661(1997)
J.-K. Hwang & A. Warshel, On the relationship between the dispersed polaron and spin-boson models. Chem. Phys. Lett. 271, 223-225 (1997).
J.-K. Hwang & A. Warshel, How important are quantum mechanical nuclear motions in enzyme catalysis. J. Am. Chem. Soc. 118, 11745 (1996).
J.-K. Hwang & J.-J. Pan, A Classical Trajectory Mapping Approach for Simulations of Chemical Reactions in Solution and in Enzymes. J. Phys. Chem. 100, 909 (1996)
J.-J. Pan & J.-K. Hwang, Mixed Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution and in Enzymes, in Biocomputing '96, edited by Lawrence Hunter and Teri E. Klein. (World Scientific, Singapore, 1996) p.539-549.
J.-K. Hwang & J.-J. Pan, Simulation of Chemical Reactions in Solution by a Combination of Chemical and Quantum Mechanical Approach. Chem. Phys. Lett. 243, 171-175 (1995).

J.-K. Hwang & W.-F. Liao, Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng., 8, 363-370 (1995).
J.-K. Hwang & A. Warshel, A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants. J. Phys. Chem. 97, 10053-10058 (1993) .
A. Warshel, J.-K. Hwang and J. Åqvist, Computer Simulations of Enzymatic reactions: Examination of Linear Free-Energy Relationships and Quantum-mechanical Corrections in the Initial Proton-Transfer Step of Carbonic Anhydrase. Faraday Discuss. 93, 225-238 (1992).
J-K. Hwang, Z. T. Chu, A. Yadav and A. Warshel, Simulations of Quantum Mechanical Corrections for Rate Constants of Hydride-transfer Reactions in Enzymes and Solutions. J. Phys. Chem. 95 8445 (1991).
A. Warshel, G. Naray-Szabo, F. Sussman & J-K. Hwang, in Perspectives in Biochemitsry Vol II, edited by Hans Neurath, (American Chemical Society , p. 115 (1991).
A. Warshel, Z. T. Chu & J-K. Hwang, The Dynamics of the Primary event in rhodopsins revisted. Chem. Phys. 158 303 (1991).
A. Warshel, G. Naray-Szabo, F. Sussman & J-K. Hwang, How Do Serine Proteases Really Work? Biochemistry 28 3629 (1989).
J-K. Hwang and A. Warshel, Why Ion Pair Reversal by Protein Engineering is Unlikely to Succeed. Nature, 334 270 (1988).
A. Warshel, F. Sussman and J-K. Hwang, Evaluation of Catalytic Free Energies in Genetically Modified Proteins. J. Mol. Biol. 201 139 (1988).
S. Creighton, J-K Hwang, A. Warshel, W. W. Parson and J. Norris, Simulating The Dynamics of the Primary Charge Separation Process in Bacterial Photosynthesis. Biochemistry 27 774 (1988).
J-K Hwang, S. Creighton, G. King, D. Whitney, and A. Warshel, Effects of Solute-Solvent Coupling and Solvent Saturation on Solvation Dynamics of Charge Transfer Reactions. J. Chem. Phys. 89 859 (1988).
J-K Hwang, F. Sussman, and A.Warshel, Simulating the Energetics and Dynamics of Enzymatic Reactions in Genetically Modified Enzymes. in Structure and Expression, edited by R.H Sarma and M.H. Sarma (Adenine Press,New York 1988), p. 95.
J-K Hwang, G. King, S. Creighton and A. Warshel, Simulation of Free Energy Relationships and Dynamics of SN2 Reactions in Aqueous Solutions. J. Am. Chem. Soc. 110 5297 (1988).
J.-K. Hwang & A. Warshel, Semiquantitative Calculations of Catalytic Free energies in Genetically Modified Subtilisin. Biochemistry, 26, 2669 (1987).
J.-K. Hwang & A. Warshel, Microscopic Examination of Free-Energy Relationships for Electron Transfer in Polar Solvents. J. Am. Chem. Soc. 109, 715 (1987).
A. Warshel & J.-K. Hwang, Simulation of the Dynamics of Electron Transfer Reactions in Polar Solvents: Semiclassical Trajectories and Dispersed Polaron Approaches. J. Chem. Phys. 84, 4938 (1986).
A. Warshel & J.-K. Hwang, Quantized Semiclassical Trajectory Approach for Evaluation of Vibronic Transitions in Anharmonic Molecules. J. Chem. Phys. 82, 1756(1985).
J.-K. Hwang & A. Warshel, Semiclassical Simulation of the Spectra of Anharmonic Molecules: Problems and Alternatives. Chem. Phys. Lett. 115, 182 (1985).
J.-K. Hwang & A. Warshel, A Shortcut for Multidimensional Quantization. The Average Partial Action Method. Chem. Phys. Lett. 118, 289 (1985).
J.-K. Hwang, G.-C. Yen & L. S. Hwang, Detection of Vegetable Oil Adulteration by HPLC Analysis of Triglycerides. J. Chin. Agric. Chem. Soc. 91, 20 (1982).

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