1. Tzou, W.-S., Hwang, M.-J., (1997)
¡§A Model for Fis N-Terminus
and Fis-Invertase Recognition,¡¨ FEBS Lett. 401:1-5. (NSC
85-2311-B-001-030-B16).
2. Yang, P.-K., Lee, C.-Y., Hwang, M.-J.,
(1997) ¡§Shaker Pore Structure
as Predicted by Annealed Atomic Simulation Using Symmetry and Novel Geometric
Restraints,¡¨ Biophys. J. 72:2479-2489 (NSC 85-2113-M-001-011 &
86-2314-B-001-035).
3. Tzou, W.-S., Hwang, M.-J., (1997)
"Introduction to Protein Structure Predictions," (in Chinese) Chemistry
(The Chinese Chem. Soc., Taiwan China), 55:101-109.
4. Peng, Z., Ewig, C.S., Hwang, M.-J.,
Waldman, M., Hagler, A.T., (1997) ¡§Derivation of Clase II Force Fields. 4. van der Waals
Parameters of Alkali Metal Cations and Halide Anions,¡¨ J. Phys. Chem., 101: 7243-7252.
5. Maple, J.R., Hwang, M.-J., Jalkanen,
K.J., Stockfisch, T.P., Hagler, A.T., (1998) ¡§Derivation of Class II Force Fields. 5. Quantum
Force Field for Amides, Peptides, and Related Compounds,¡¨ J. Comput. Chem.,19:430-458.
6. Hwang, M.-J., Ni, X., Waldman, M., Ewig, C.S., Hagler, A.T.,
(1998) ¡§Derivation of
Class II Force Fields. 6. Carbohydrate Compounds and Anomeric Effects,¡¨ Biopolymers. 45:435-468.
7. Chu, P.-Y., Hwang, M.-J., (1998) ¡§New Insights for Dinucleotide Backbone
Binding in Conserved C5¡¦-H¡KO Hydrogen Bonds,¡¨ J. Mol. Biol. 279:695-701.
8. Lee, C.-Y., Yang, P.-K., Tzou, W.-S., Hwang,
M.-J., (1998) ¡§Estimates
of Binding Free Energies for HIV Protease Inhibitors Using Different Levels of
Approximations,¡¨ Protein
Eng.11:429-437 (NSC86-2811-B-001-0029).
9. Lin, W.-J., Hwang, M.-J. (1998)
¡§VHMPT: a graphical Viewer
and editor for Helical Membrane Protein Topologies,¡¨ Bioinformatics, 14:866-868.
10. Cheng, Y.-S., Tang, T.K., Hwang, M.-J.
(1999) ¡§Amino
Acid Conservation and Clinical Severity of Human Glucose-6-Phosphate Dehydrogenase
Mutations,¡¨ J. Biomed.
Sci. 6:106-114 (NSC87-2314-B-001-034).
11. Tzou, W.-S., Hwang, M.-J. (1999)
¡§Modeling Helix-Turn-Helix
Protein-Induced DNA Bending with Knowledge-Based Distance Restraints,¡¨ Biophys. J., 77: 1191-1205.
12. Lai, H.-L., Lin, T.-H., Kao, Y.-Y., Lin,
W.-J., Hwang, M.-J., Chern, Y. (1999) ¡§The N-Terminal Domain of Type VI Adenylyl
Cyclase Mediates Its Inhibition by Protein Kinase C,¡¨ Mol. Pharmacol., 56:
644-650.
13. Yang, P.-K., Tzou, W.-S., Hwang, M.-J.
(1999) ¡§Restraint-Driven
Formation of Ą-Helical
Coiled Coils in Molecular Dynamics Simulations,¡¨ Biopolymers, 50: 667-677
(NSC85-2113-M-001-011).
14. Hwang, M.-J., Chu, P.-Y., Chen, J.-C., Chao, I. (1999) ¡§Conformational Analysis of Three Pyrophosphate
Model Species: Diphosphate, Methyl Diphosphate, and Triphosphate,¡¨ J. Comput. Chem., 20: 1702-1715 (NSC86-2811-B-001-022).
15. Chen, J.-W., Luo, Y.-L., Hwang, M.-J.*,
Peng, F.-C., Ling, K.-H.* (1999) ¡§Territrem B, a tremorgenic mycotoxin that inhibits acetylcholinesterase
with a non-covalent yet irreversible binding mechanism,¡¨ J. Biol. Chem., 274:34916-34923.(*corresponding authors)
16. Liu, C.L., Tsai, C.C., Lin, S.C., Wang,
L.I., Hsu, C.I., Hwang, M.-J., Lin, J.Y. (2000) ¡§Primary Structure and Function Analysis
of the Abrus precatorius Agglutinin A Chain by Site-directed
Mutagenesis,¡¨ J.
Biol. Chem., 275: 1897-1901.
17. Yao, P.-L.; Hwang, M.-J.*; Chen, Y.-M.; Yeh,
K.-W.* (2001) ¡§Site-Directed
Mutagenesis Evidence for a Negatively Charged Trypsin Inhibitory Loop in Sweet Potato Sporamin.¡¨ FEBS Lett., 496: 134-138 (*corresponding authors).
18. Ewig, C. S., Berry, R., Dinur, U., Hill,
J.R., Hwang, M.-J., Li, H., Liang, C., Maple, J., Peng, Z.W., Stockfisch,
T.P., Thacher, T.S., Yan, L., Ni, X., Hagler, A.T. (2001) ¡§Derivation of Class II Force Fields. VIII.
Derivation of a General Quantum Mechanical Force Field for Organic Compounds.¡¨ J. Comput. Chem., 22:1782-1800.
19. Lin, T.H., Lai, H.L., Kao, Y.Y., Sun,
C.N., Hwang, M.-J., Chern, Y. (2002) ¡§Protein Kinase C Inhibits Type VI Adenylyl
Cyclase (ACVI) by Phosphorylating the Regulatory N Domain and Two Catalytic C1
and C2 Domains.¡¨ J.
Biol. Chem.277: 15721-15728
20. Chen, L.Y.Y., Lu, S.H., Shih, S.C., Hwang, M.-J. (2002)
¡§Single Nucleotide
Polymorphism Mapping Using Genome-wide Unique Sequences.¡¨ Genome Research 12: 1106-1111
21.Yang, J.M.*, Tsai, C.H., Hwang, M.-J.*,
Tsai, H.K., Hwang J.K., Kao, C.Y. (2002) ¡§GEM: a Guassian Evolutionary Method for Predicting
Protein Side-chain Conformations.¡¨ Protein Sci. 11: 1897-1907
(*corresponding authors)
22.Shih, Edward S.C., Hwang, M.-J.
(2003) "Protein Structure Comparison by Probability-Based
Matching of Secondary Structure Elements." Bioinformatics 19:735-741.
23. Chen, M.-C., Hwang,
M.-J., Chou, Y.-C., Chen, W.-H., Cheng, G.,Nakano, H., Luh, T.-Y., Mai,
S.-C., Hsieh, S.-L. (2003) "The Role of ASK1 in Lymphotoxin-beta
Receptor-Mediated Cell Death." J. Biol. Chem., 278:16073-16081.
24. Yeh CS, Chen FM, Wang JY, Cheng TL, Hwang MJ, Tzou WS. (2003)
"Directional Shape Complementarity at The Protein-DNA Interface."
J. Mol. Recognit., 16(4): 213-222
25. Shih SR, Chiang C, Chen TC, Wu CN, Hsu JT, Lee JC, Hwang MJ,Li ML, Chen GW, Ho MS (2004)
"Mutations at KFRDI and VGK domains of enterovirus 71 3C protease affect its RNA binding and proteolytic activities."
J Biomed Sci. 11(2):239-248
26. Shih E. S, Hwang M.-J. (2004)
"Alternative Alignments from Comparison of Protein Strutures."
Proteins: Structure, Function and Bioinformatics 56: 519-527
27. Lee I.-Y., Soong T.-T., Ho J.-M., Hwang M.-J. (2004)
"Derivation and Analysis of Fragment Libraries of Protein Structures."
Fourth IEEE Symposium on Bioinformatics and Bioengineering (BiBE'04), Taichung, Taiwan. May 19-21, pp516-521
28. Kao Y.-Y., Lai H.-L., Hwang M.-J., Chern Y. (2004)
"An Important functional role of the N terminus domain of type VI adenylyl cyclase (ACVI) in Gia-mediated inhibition."
J Biol Chem. 279: 34440-34448
29. Liao B.-Y., Chang Y.-J., Ho J.-M., Hwang M.-J. (2004)
"The UniMarker (UM) Method for Synteny Mapping of Large Genomes."
Bioinformatics 20: 3156-3165
30. Soong, T.-T., Hwang M.-J., Chen, C.-M. (2004) "Discovery of
Recurrent Structural Motifs for Approximating Three-Dimensional Protein
Structures."
J. Chin. Chem. Soc. 51: 1107-1114
31. Wang, S.-L., Chen, C.-M., Hwang M.-J. (2005) "Classification of
Protein 3D Folds by Hidden Markov Learning on Sequences of Structural
Alphabets.
"
Proceedings of The Third Asia-Pacific Bioinformatics
Conference, Singapore, January 17-21.
pp65-72
32. Xie, Z.-R., Hwang M.-J. (2006) "A New Neural Network for B-Turn
Predictions: The Effect of Site-Specific Amino Acid Preference."
Proceedings of The Fourth Asia-Pacific Bioinformatics Conference, Taipei,
February 13-16.
pp237-246
33. Pao, S.-Y, Lin, W.-L, Hwang M.-J. (2006) "In silico
identification and comparative analysis of differentially expressed genes in
human and mouse tissues.
"
BMC Genomics, 7:86
34. Shih, E.S.C., Gan, R.-C., Hwang M.-J. (2006) "OPAAS: a web
server for Optimal, Permuted, and other Alternative Alignments of protein
Structures.
"
Nucleic Acids Research (web server issue) W95-W98
35. Chang, D.T.H., Weng, Y.-Z., Lin, J.-H., Hwang M.-J., Oyang, Y.-J. (2006) "Protemot: prediction of protein-binding sites with automatically
extracted geometrical templates.
"
Nucleic Acids Research (web server issue) W303-W309
36. Liu W.C., Lin W.H., Davis A.J., Jordan F., Yang H.T. Hwang M.J. (2007)
"A network perspective on the topological importance of enzymes and their phylogenetic conservation."
BMC Bioinformatics 8:121
37. Xie, Z.R., Yang, H.T., Liu, W.C., Hwang M.J. (2007)
"The role of microRNA in the delayed negative feedback regulation of gene expression."
BBRC 358:722-726
38. Yang, H.-t., Hsu, C.-P., Hwang M.J. (2007)
"An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors."
The Journal of Biochemistry (Tokyo) 142: 135-144