PUBLICATIONS
Over 452 peer-review scientific papers. As of December 2012, Professor Kuo-Chen Chou's publications have been cited more than 23,789 times with h-index of 83, according to ISI Science Citation Index (Web of Science). For more recent information about this, click his ResearchID.

According to the report from Science Watch, Dr. Kuo-Chen Chou has been named the author with the highest number of Hot Papers in the world during 2007-2008.

A. Selected Papers

1. Chou, K.C. (2013). Invited Review: Some Remarks on Predicting Multi-Label Attributes in Molecular Biosystems. Molecular BioSystems, in press.
2. Chen, W., Feng, P. M., Lin, H. & Chou, K.C. (2013). iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Research, doi:10.1093/nar/gks1450
3. Xiao, X., Wang, P., Lin, W. Z., Jia, J. H. & Chou, K.C. (2013). iAMP-2L: A two-level multi-label classifier for identifying antimicrobial peptides and their functional types. Analytical Biochemistry, doi:10.1016/j.ab.2013.01.019
4. Lin, W.Z., Fang, J.A., Xiao, X. & Chou, K.C. (2013). iLoc-Animal: A multi-label learning classifier for predicting subcellular localization of animal proteins Molecular BioSystems, doi:10.1039/C3MB25466F
5. Xu, Y., Ding, J., Wu, L.Y. & Chou, K.C. (2013). iSNO-PseAAC: Predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition PLoS ONE, 8, e55844. doi:10.1371/journal.pone.0055844
6. Chen, W., Lin, H., Feng, P. M., Ding, C., Zuo, Y. C. & Chou, K.C. (2012). iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties. PLoS ONE, 7, e47843. doi:10.1371/journal.pone.0047843
7. Lin, W. Z., Fang, J. A., Xiao, X. & Chou, K.C. (2012). Predicting Secretory Proteins of Malaria Parasite by Incorporating Sequence Evolution Information into Pseudo Amino Acid Composition via Grey System Model. PLoS One, 7, e49040. doi:10.1371/journal.pone.0049040
8. Ma, Y., Wang, S. Q., Xu, W. R., Wang, R. L. & Chou, K.C. (2012). Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach. PLoS One, 7, e38546. doi:10.1371/journal.pone.0038546
9. Chou, K.C., Wu, Z. C. & Xiao, X. (2012). iLoc-Hum: Using accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites. Molecular BioSystems, 8, 629-641. doi:10.1039/c1mb05420a
10. Li, B.Q., Huang, T., Liu, L., Cai, Y.D. & Chou, K.C. (2012). Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network. PLoS ONE, 7, e33393. doi:10.1371/journal.pone.0033393
11. Huang, T., Wang, J., Cai, Y.D., Yu, H. & Chou, K.C. (2012). Hepatitis C Virus Network Based Classification of Hepatocellular Cirrhosis and Carcinoma. PLoS ONE, 7, e34460. doi:10.1371/journal.pone.0034460
12. Xiao, X., Wang, P. & Chou, K.C. (2012). iNR-PhysChem: A Sequence-Based Predictor for Identifying Nuclear Receptors and Their Subfamilies via Physical-Chemical Property Matrix. PLoS ONE, 7, e30869. doi:10.1371/journal.pone.0030869
13. Li,B.Q., Hu, L.L., Niu,S., Cai, Y.D. & Chou,K.C. (2012). Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches. Journal of Proteomics, 75, 1654-1665. doi:10.1016/j.jprot.2011.12.003
14. 14. Chen, L., Zeng, W. M., Cai, Y. D., Feng, K. Y. & Chou,K.C. (2012). Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities. PLoS ONE, 17, e35254. doi:10.1371/journal.pone.0035254
15. Wang, J.F. & Chou,K.C. (2012). Insights into the Mutation-Induced HHH Syndrome from Modeling Human Mitochondrial Ornithine Transporter-1. PLoS One, 7, e31048. doi:10.1371/journal.pone.0031048
16. Huang, T., Zhang, J., Xu, Z. P., Hu, L.L., Chen, L., Shao, J. L., Zhang, L., Kong, X. Y., Cai, Y.D. & Chou,K.C. (2012). Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches. Biochimie, 94, 1017-1025. doi:10.1016/j.biochi.2011.12.024
17. Chou, K.C. (2011) Some remarks on protein attribute prediction and pseudo amino acid composition (50th Anniversary Year Review). Journal of Theoretical Biology, 273, 236-247. doi:10.1016/j.jtbi.2010.12.024
18. Li, X. B., Wang, S. Q., Xu, W. R., Wang, R. L. & Chou, K.C. (2011). Novel Inhibitor Design for Hemagglutinin against H1N1 Influenza Virus by Core Hopping Method. PLoS One, 6, e28111. doi:10.1371/journal.pone.0028111
19. Huang, T., Chen, L., Cai, Y.D. & Chou, K.C.(2011). Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PLoS ONE, 6, e25297. doi:10.1371/journal.pone.0025297
20. Wang, P., Xiao, X. & Chou, K.C. (2011). NR-2L: A Two-Level Predictor for Identifying Nuclear Receptor Subfamilies Based on Sequence-Derived Features. PLoS ONE, 6, e23505. doi:10.1371/journal.pone.0023505
21. Lin, W. Z., Fang, J.A., Xiao, X. & Chou, K.C.(2011). iDNA-Prot: Identification of DNA binding proteins using random forest with grey model. PLoS ONE, 6, e24756. doi:10.1371/journal.pone.0024756
22. Wu, Z.C., Xiao, X. & Chou, K.C.(2011). iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sitesw. Molecular BioSystems, doi:10.1039/c1mb05232b
23. Xiao, X., Wu, Z.C. & Chou, K.C.(2011). A multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites. PLoS One, 6, e20592. doi:10.1371/journal.pone.0020592
24. Lian, P., Wi, D. Q., Wang, J. F. & Chou, K.C.(2011). An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS ONE, 6, e18587. doi:10.1371/journal.pone.0018587
25. Xiao, X., Wu, Z.C. & Chou, K.C.(2011). iLoc-Virus: A multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites. Journal of Theoretical Biology, 284, 42-51. doi:10.1016/j.jtbi.2011.06.005
26. Wang, J. F. & Chou, K.C.(2011). Insights from modeling the 3D structure of New Delhi metallo-beta-lactamase and its binding interactions with antibiotic drugs. PLoS ONE, 6, e18414. doi:10.1371/journal.pone.0018414
27. Chou, K. C., Wu, Z. C. & Xiao, X. (2011). iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS ONE, 6, e18258. doi:10.1371/journal.pone.0018258
28. Xiao, X., Wang, P. & Chou, K. C. (2011). GPCR-2L: Predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions. Molecular BioSystems, 7, 911-919. doi:10.1039/c0mb00170h
29. Chou, K. C. & Shen, H. B. (2010). Cell-PLoc 2.0: An improved package of web-servers for predicting subcellular localization of proteins in various organisms. Natural Science, 2, 1090-1103 (openly accessible at http://www.scirp.org/journal/NS/). doi: 10.4236/ns.2010.210136
30. Wu, Z.C., Xiao, X. & Chou, K.C.(2010). 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. Journal of Theoretical Biology, 267, 29-34. doi: 10.1016/j.jtbi.2010.08.007 2D-MH web server at http://icpr.jci.edu.cn/bioinfo/pplot/2D-MH
31. Chou, K.C.(2010) Graphic rule for drug metabolism systems. Current Drug Metabolism, 11, 369-378. doi:10.2174/138920010791514261
32. Chou K.C., Shen H.B. (2010) Plant-mPLoc: A top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE, 5, e11335. doi:10.1371/journal.pone.0011335
33. Chou, K. C. & Shen, H. B. (2010) A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS ONE, 2010, 5, e9931. doi:10.1371/journal.pone.0009931 Euk-mPLoc 2.0 web server at http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/
34. He, Z.S., Zhang, J., Shi, X.H., Hu, L.L., Kong, X.G., Cai, Y.D. & Chou, K. C. (2010). Predicting drug-target interaction networks based on functional groups and biological features. PLoS ONE, 5, e9603. doi:10.1371/journal.pone.0009603
35. Chou, K. C. (2009). Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology. Current Proteomics, 6, 262-274. doi:10.2174/157016409789973707
36. Chou, K. C. & Shen, H. B. (2009). Review: recent advances in developing web-servers for predicting protein attributes. Natural Science 2, 63-92. doi: 10.4236/ns.2009.12011
37. Wang, J. F. & Chou, K. C. (2009). Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem Biophys Res Comm, 390, 608-612. doi:10.1016/j.bbrc.2009.10.014
38. Shen, H. B. & Chou, K. C. (2009). A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. Analytical Biochemistry 394, 269-274. doi:10.1016/j.ab.2009.07.046 Hum-mPLoc 2.0 web server at http://www.csbio.sjtu.edu.cn/bioinf/hum-multi-2/.
39. Chou, K. C. (2009). Automated prediction of protein attributes and its impact to biomedicine and drug discovery. In Automation in Proteomics and Genomics: An Engineering Case-Based Approach (for Harvard/MIT interdisciplinary special studies courses), Chap.5, pp.97-143. (Alterovitz, G., Benson, R., and Ramoni, M.F. ed.), John Wiley & Sons Ltd., West Sussex, UK.
40. Xiao, X., Wang, P. & Chou, K.C.(2009). GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. Journal of Computational Chemistry 30, 1414-1423. GPCR-CA web server at http://icpr.jci.jx.cn/bioinfo/GPCR-CA. doi:10.1002/jcc.21163
41. Chou, K. C. & Shen, H. B. (2008). Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nature Protocols, 3, 153-162. doi:10.1038/nprot.2007.494 Cell-PLoc web server at http://http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc/
42. Chou, K. C. & Shen, H. B. (2007). Review: Recent progresses in protein subcellular location prediction. Analytical Biochemistry, 370, 1-16. doi:10.1016/j.ab.2007.07.006
43. Huang, R. B., Du, Q. S., Wang, C. H. & Chou, K. C. (2008). An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem. Biophys. Res. Comm., 377, 1243-1247. doi:10.1016/j.bbrc.2008.10.148
44. Chou, K. C. and Shen, H.B. (2008) ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem Biophys Res Comm, 376, 321-325. doi:10.1016/j.bbrc.2008.08.125 ProtIdent web server at http://www.csbio.sjtu.edu.cn/bioinf/Protease/
45. Chou, K.C.& Shen, H.B. (2007) MemType-2L: A Web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM, Biochem Biophys Res Comm, 360, 339-345; doi:10.1016/j.bbrc.2007.06.027 MemType-2L web server at http://chou.med.harvard.edu/bioinf/MemType/
46. Chou, K.C.& Shen, H.B. (2007). Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Comm, 357, 633-640. doi:10.1016/j.bbrc.2007.03.162 Signal-CF web server at http://chou.med.harvard.edu/bioinf/Signal-CF/
47. Chou, K.C.& Shen, H.B. (2007) Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. Journal of Proteome Research, 6, 1728-1734; doi:10.1021/pr060635i Euk-mPLoc web server at http://chou.med.harvard.edu/bioinf/euk-multi/
48. Chou, K.C.(2005). Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. Journal of Proteome Research, 4, 1681-1686. doi:10.1021/pr050145a
49. Chou, K.C.(2005). Insights from modeling the 3D structure of DNA-CBF3b complex. Journal of Proteome Research, 4, 1657-1660. doi:10.1021/pr050135+
50. Chou, K.C.(2005) Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes, Bioinformatics, 21, 10-19. doi:10.1093/bioinformatics/bth466
51. Chou, K.C.(2004) Molecular therapeutic target for type-2 diabetes, Journal of Proteome Research, 3, 1284-1288. doi:10.1021/pr049849v
52. Chou, K.C.(2004). Insights from Modelling the 3D Structure of the extracellular domain of alpha-7 nicotinic acetylcholine receptor. Biochem. Biophys. Res. Comm., 319, 433-438. doi:10.1016/j.bbrc.2004.05.016
53. Chou, K.C.(2004). Review: Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11, 2105-2134. PMID:15279552
54. Chou, K.C.(2004). Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Comm. 316, 636-642. doi:10.1016/j.bbrc.2004.02.098
55. Chou, K.C., Wei, D.Q., and Zhong, W.Z. (2003). Binding mechanism of coronavirous main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Comm. 308, 148-151. doi:10.1016/S0006-291X(03)01342-1
56. Cai, Y.D., Zhou, G.P., and Chou, K.C. (2003). Support vector machines for predicting membrane protein types by using functional domain composition, Biophysical Journal 84, 3257-3263. doi:10.1016/S0006-3495(03)70050-2
57. Chou, K.C.and Cai, Y.D. (2002). Using functional-domain composition and support vector machines for prediction of protein subcellular location, Journal of Biological Chemistry 29, 45765-45769. doi:10.1074/jbc.M204161200
58. Chou, K.C.(2001). Prediction of protein cellular attributes using pseudo-amino-acid-composition. PROTEINS: Structure, Function, and Genetics 43, 246-255. doi:10.1002/prot.1035
59. Chou, K. C. (2000). Review: Prediction of tight turns and their types in proteins. Analytical Biochemistry 286, 1-16. doi:10.1006/abio.2000.4757
60. Chou, K. C., Tomasselli, A.G., and Heinrikson, R.L. (2000). Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Letters 470, 249-256. doi:10.1016/S0014-5793(00)01333-8
61. Chou, K.C. & Elrod, D.W. (1999). Protein subcellular location prediction. Protein Engineering 12, 107-118. doi:10.1093/protein/12.2.107
62. Chou, K.C.(1996). Review: Prediction of HIV protease cleavage sites in proteins. Analytical Biochemistry 233, 1-14. doi:10.1006/abio.1996.0001
63. Chou, K.C.and Zhang, C.T. (1995). Review: Prediction of protein structural classes. Critical Reviews in Biochemistry and Molecular Biology 30, 275-349. doi:10.3109/10409239509083488
64. Chou, K.C.(1995). A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Structure, Function and Genetics 21, 319-344. doi:10.1002/prot.340210406
65. Chou, K.C. & Zhang, C.T. (1994). Predicting protein folding types by distance functions that make allowances for amino acid interactions. Journal of Biological Chemistry 269, 22014-22020. PMID:8071322
66. Chou, K.C.(1993). A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. Journal of Biological Chemistry 268, 16938-16948. PMID:8349584
67. Chou, K.C.(1992). Energy-optimized structure of antifreeze protein and its binding mechanism. Journal of Molecular Biology 223, 509-517. doi:10.1016/0022-2836(92)90666-8
68. Chou, K.C., Maggiora, G.M. and Scheraga, H.A. (1992). The role of loop-helix interactions in stabilizing four-helix bundle proteins. Proceedings of National Academy of Sciences, USA 89, 7315-7319. doi:10.1073/pnas.89.16.7315
69. Chou, K.C., Carlacci, L. and Maggiora, G.M. (1990). Conformational and geometrical properties of idealized beta-barrels in proteins. Journal of Molecular Biology 213, 315-326. doi:10.1016/S0022-2836(05)80193-7
70. Chou, K.C., Nemethy, G. and Scheraga, H. A. (1990). Review: Energetics of interactions of regular structural elements in proteins. Accounts of Chemical Research 23, 134-141. doi:10.1021/ar00173a003
71. Chou, K.C.(1990). Review: Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophysical Chemistry 35, 1-24. doi:10.1016/0301-4622(90)80056-D
72. Chou, K. C. (1989). Graphical rules in steady and non-steady enzyme kinetics. Journal of Biological Chemistry 264, 12074-12079. PMID:2745429
73. Chou, K. C. (1989). Low-frequency resonance and cooperativity of hemoglobin. Trends in Biochemical Sciences 14, 212. doi:10.1016/0968-0004(89)90026-1
74. Chou, K. C., Maggiora, G. M. and Mao, B. (1989). Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA. Biophysical Journal 56, 295-305. doi:10.1016/S0006-3495(89)82676-1
75. Chou, K. C., Maggiora, G. M., Nemethy, G. and Scheraga, H. A. (1988). Energetic approach to 4-alpha-helix packing. Proceedings of National Academy of Sciences, USA 85, 4295-4299. PMID:3380793
76. Chou, K. C. (1988). Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry 30, 3-48. doi:10.1016/0301-4622(88)85002-6
77. Chou, K. C. (1984). Low-frequency vibration of DNA molecules. Biochemical Journal 221, 27-31. PMID:6466317
78. Chou, K. C., Nemethy, G. and Scheraga, H. A. (1984). Energetic approach to packing of alpha-helices: 2. General treatment of nonequivalent and nonregular helices. Journal of American Chemical Society 106, 3161-3170. doi:10.1021/ja00323a017
79. Chou, K. C. (1984). The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophysical Journal 45, 881-890. doi:10.1016/S0006-3495(84)84234-4
80. Chou, K. C., Nemethy, G. and Scheraga, H. A. (1983). Role of interchain interactions in the stabilization of right-handed twist of beta-sheets. Journal of Molecular Biology 168, 389-407. PMID:6887247
81. Chou, K. C. and Scheraga, H. A. (1982). Origin of the right-handed twist of beta-sheets of poly-L-valine chains. Proceedings of National Academy of Sciences, USA 79, 7047-7051. doi:10.1073/pnas.79.22.7047
82. Chou, K. C. and Zhou, G. P. (1982). Role of the protein outside active site on the diffusion-controlled reaction of enzyme. Journal of American Chemical Society 104, 1409-1413. doi:10.1021/ja00369a043
83. Chou, K. C. (1976). The kinetics of the combination reaction between enzyme and substrate. Scientia Sinica 19, 505-528. PMID:824728
84. Chou, K. C. and Jiang, S. P. (1974). Studies on the rate of diffusion-controlled reactions of enzymes. Scientia Sinica 17, 664-680. PMID:4219062

B. List of Others

85. Zheng, L. L., Li, Y. X., Ding, J., Guo, X. K., Feng, K. Y., Wang, Y. J., Hu, L. L., Cai, Y. D., Hao, P. & Chou, K.C. (2012). A comparison of computational methods for identifying virulence factors. PLoS One, 7, e42517. doi:10.1371/journal.pone.0042517
86. Li, B. Q., Hu, L. L., Chen, L., Feng, K. Y., Cai, Y. D. & Chou, K.C. (2012). Prediction of Protein Domain with mRMR Feature Selection and Analysis. PLoS One, 7, e39308. doi:10.1371/journal.pone.0039308
87. Xiao, X., Lin, W. Z. & Chou, K.C. (2012). Recent advances in predicting G-protein coupled receptor classification. Current Bioinformatics, 7, 132-142.
88. Niu, S., Hu, L. L., Zheng, L. L., Huang, T., Feng, K. Y., Cai, Y. D., Lie, H. P., Li, Y. X. & Chou, K.C. (2012).Predicting protein oxidation sites with feature selection and analysis approach. Journal of Biomolecular Structure and Dynamics, 29, 1154-1162. doi:10.1080/07391102.2011.672629
89. Hu, L. L., Feng, K. Y., Cai, Y.D. & Chou, K.C. (2012). Using Protein-protein Interaction Network Information to Predict the Subcellular Locations of Proteins in Budding Yeast. Protein & Peptide Letters, 19, 644-751. PMID:22519536
90. Wang, J. F. & Chou, K.C. (2012). Recent advances in computational studies on influenza a virus M2 proton channel. Mini-Reviews in Medicinal Chemistry, 12, 971-978. PMID:22303978
91. Zhang, T., Wei, D. Q. & Chou, K.C. (2012). A Pharmacophore Model Specific to Active Site of CYP1A2 with a Novel Molecular Modeling Explorer and CoMFA. Medicinal Chemistry. 8, 198-207. PMID:22385179
92. Li, J., Wei, D. Q., Wang, J. F., Yu, Z. T. & Chou, K.C. (2012). Molecular Dynamics Simulations of CYP2E1. Medicinal Chemistry, 8, 208-221. PMID:22385180
93. Wu, Z. C., Xiao, X. & Chou, K.C. (2012). iLoc-Gpos: A Multi-Layer Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Gram-Positive Bacterial Proteins. Protein & Peptide Letters, 19, 4-14. PMID:21919865
94. Li, L., Wei, D. Q., Wang, J. F. & Chou, K.C. (2012). SCYPPred: A Web-Based Predictor of SNPs for Human Cytochrome P450. Protein & Peptide Letters, 19, 57-61. PMID:21919859
95. Pugalenthi, G., Kandaswamy, K. K., Chou, K.C. , Vivekanandan, S. & Kolatkar, P. (2012). RSARF: Prediction of Residue Solvent Accessibility from Protein Sequence Using Random Forest Method. Protein & Peptide Letters, 19, 50-56. PMID:21919860
96. Yi, X. F., He, Z. S., Chou, K.C. & Kong, X. Y. (2012). Nucleosome positioning based on the sequence word composition. Protein & Peptide Letters, 19, 79-90. PMID:21919856
97. Cai, L., Huang, W. & Chou, K.C. (2012). Prostate Cancer with Variants in CYP17 and UGT2B17 Genes: A Meta-Analysis. Protein & Peptide Letters, 19, 62-69. PMID:21919858
98. He, Z. S., Shi, X. H., Kong, X. Y., Zhu, Y. B. & Chou, K.C. (2012). A novel sequence-based method for phosphorylation site prediction with feature selection and analysis. Protein & Peptide Letters, 19, 70-78. PMID:21919857
99. Huang, T., Cai, Y. D., Chen, L., Hu, L. L., Kong, X. Y., Li, Y. X. & Chou, K.C. (2012). Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles. Protein & Peptide Letters, 19, 113-119. PMID:21919852
100. Chou, K.C. , Lin, W.Z. & Xiao, X. (2011). Wenxiang: a web-server for drawing wenxiang diagrams. Natural Science, 3, 862-865 (openly accessible at http://www.scirp.org/journal/NS/). doi:10.4236/ns.2011.310111
101. Gao, L., Dai, H., Zhang, T.L., & Chou, K.C. (2011). Remote data retrieval for bioinformatics applications: an agent migration approach. PLoS ONE, 6, e20949. doi:10.1371/journal.pone.0020949
102. Hu, L., Huang, T., Cai, Y. D. & Chou, K.C. (2011). Prediction of body fluids where proteins are secreted into based on protein interaction network. PLoS ONE, 6, e22989. doi:10.1371/journal.pone.0022989
103. Huang, T., Niu, S., Xu, Z.P., Huang, Y., Kong, X.Y., Cai, Y. D. & Chou, K.C. (2011). Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties. PLoS ONE, 6, e22940. doi:10.1371/journal.pone.0022940
104. He, J., Wei, D.Q., Wang, J.F. & Chou, K.C. (2011). Predicting protein-ligand binding sites based on an improved geometric algorithm. Protein & Peptide Letters, 18, 997-1001. doi:10.2174/092986611796378756
105. Liu, X.Y., Wang, R.L., Xu, W.R., Tang, L.D., Wang, S.Q. & Chou, K.C. (2011). Docking and molecular dynamics simulations of peroxisome proliferator activated receptors interacting with Pan Agonist Sodelglitazar. Protein & Peptide Letters, 18, 1021-1027. doi:10.2174/092986611796378701
106. Wang, P., Hu, L., Liu, G., Jiang, N., Chen, X., Xu, J., Zheng, W., Li, L., Tan, M., Chen, Z., Song, H., Cai, Y. D. & Chou, K.C. (2011). Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS ONE, 6, e18476. doi:10.1371/journal.pone.0018476
107. Du, Q.S., Wei, H., Huang, R.B. & Chou, K.C. (2011). Progress in structure-based drug design against influenza A virus. Expert Opinion, 6, 619-631. doi:10.1517/17460441.2011.571671
108. Xiao, X. & Chou, K.C. (2011) Using pseudo amino acid composition to predict protein attributes via cellular automata and other approaches. Current Bioinformatics, 6, 251-260.
109. Hu, L., Huang, T., Shi, X., Lu, W. C., Cai, Y. D. & Chou, K.C. (2011). Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties PLoS ONE, 6, e14556. doi:10.1371/journal.pone.0014556
110. Wan, S.B., Hu, L.L., Niu, S., Wang, K., Cai, Y. D. & Chou, K.C. (2011) Identification of multiple subcellular locations for proteins in budding yeast. Current Bioinformatics, 6, 71-80.
111. Cai, L., Wang, Y., Wang, J. F. & Chou, K.C. (2011). Identification of proteins interacting with human SP110 during the process of viral infections. Medicinal Chemistry, 7, 121-126. PMID:21222611
112. Ren, L. H., Shen, Y. Z., Ding, Y. S. & Chou, K.C. (2011). Bio-entity network for analysis of protein-protein interaction networks. Asian Journal of Control, 13, 726-737. doi:10.1002/asjc.395
113. Kandaswamy, K. K., Chou, K. C., Martinetz, T., Möller, S., Suganthan, P. N., Sridharan, S. & Pugalenthi, G. (2011). AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties. Journal of Theoretical Biology, 270, 56-62. doi:10.1016/j.jtbi.2010.10.037
114. Hu, L. L., Niu, S., Shi, X. H., Cai, Y. D. & Chou, K. C. (2011). Prediction and analysis of protein palmitoylation sites Biochimie, 93, 489-496. doi:10.1016/j.biochi.2010.10.022
115. Liao, Q.H., Gao, Q.Z., Wei, J. & Chou, K.C. (2011). Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR). Medicinal Chemistry 7, 32-36. doi:10.2174/157340611794072698
116. Xiao, X., Wang, P. & Chou, K.C. (2011). Cellular automata and its applications in protein bioinformatics. Current Protein & Peptide Science, 12, 508-519. doi:10.2174/138920311796957720
117. Wen, Z.Z., Wang, Y.H., Yang, B., Xie, M.Q. & Chou, K.C. (2011). Roles of L5-7 Loop in the Structure and Chaperone Function of SsHSP14.1. Protein & Peptide Letters. 18, 275-281. doi:10.2174/092986611794578369
118. Xiao, X., Wang, P., Chou, K.C. (2011) Quat-2L: a web-server for predicting protein quaternary structural attributes. Molecular Diversity, 15, 149-155. doi:10.1007/s11030-010-9227-8
119. Chen, L., Huang, T., Shi, X. H., Cai, Y. D. & Chou, K.C. (2010). Analysis of protein pathway networks using hybrid properties. Molecules 15, 8177-8192 (Openly accessible at www.mdpi.com/journal/molecules). doi:10.3390/molecules15118177
120. Wang, S.Q., Cheng, X.C., Dong, W.L., Wang, R.L. & Chou, K.C. (2010). Three new powerful Oseltamivir derivatives for inhibiting the neuraminidase of influenza virus. Biochem Biophys Res Commun. 401, 188-191. doi:10.1016/j.bbrc.2010.09.020
121. Xie, Z., Zhang, T., Wang, J. F., Chou, K.C. & Wei, D.Q. (2010). The computational model to predict accurately inhibitory activity for inhibitors towards CYP3A4. Computers in Biology and Medicine, 40, 845-852. doi:10.1016/j.compbiomed.2010.09.004
122. Shen, Y. Z., Ding, Y. S., Gu, Q. & Chou, K.C. (2010). Identifying the Hub Proteins from Complicated Membrane Protein Network Systems. Medicinal Chemistry, 6, 165-173. PMID:20507268
123. Wang, J.F. & Chou, K.C. (2010). Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics. Protein Engineering, Design & Selection, 23, 663-666. doi:10.1093/protein/gzq040
124. Chen, L., Feng, K. Y., Cai, Y. D., Chou, K.C. , & Li, H.P. (2010). Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC-Bioinformatics, 11, 293. PMID:20513238
125. Huang, T. S., Shi, X. H., Wang, P., He, Z. S., Feng, K. Y., Hu, L. L., Kong, X. Y., Li, Y. X., Cai, Y. D. & Chou, K.C. (2010). Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE, 5, e10972. doi:10.1371/journal.pone.0010972
126. Wang, J.F., Chou, K.C. (2010). Molecular modeling of cytochrome P450 and drug metabolism. Current Drug Metabolism, 11, 342-346. PMID:20446905
127. Shen, H.B., Chou, K.C. (2010). Virus-mPLoc: A fusion classifier for viral protein subcellular location prediction by incorporating multiple sites. Journal of Biomolecular Structure and Dynamics, 28, 175-186. PMID:20645651
128. Du, Q.S., Huang, R.B., Chou, K.C. (2010). Advances in visual representation of molecular potentials. Expert Opinion on Drug Discovery, 5, 513-527. doi:10.1517/17460441.2010.484837
129. Du, Q.S., Huang, R.B., Wang, S.Q., Chou, K.C. (2010). Designing inhibitors of M2 proton channel against H1N1 swine influenza virus. PLoS ONE, 5, e9388. doi:10.1371/journal.pone.0009388
130. Shen, H.B., Chou, K.C. (2010). Gneg-mPLoc: A top-down strategy to enhance the quality of predicting subcellular localization of Gram-negative bacterial proteins. Journal of Theoretical Biology, 264, 326-333, Gneg-mPLoc web server at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/. doi:10.1016/j.jtbi.2010.01.018
131. Du, Q.S., Wang, S.Q., Huang, R.B., Chou, K.C. (2010). Computational 3D structures of drug-targeting proteins in the 2009-H1N1influenza A virus. Chemical Physics Letters, 485, 191-195. doi:10.1016/j.cplett.2009.12.037
132. Qi, J. P., Ding, Y. S., Shao, S. H., Zeng, X. H. & Chou, K.C. (2010). Cellular responding kinetics based on a model of gene regulatory networks under radiotherapy. Health 2, 137-146. doi:10.4236/health.2010.22021
133. Shen, H.B. and Chou, K.C. (2009). Gpos-mPLoc: A top-down approach to improve the quality of predicting subcellular localization of Gram-positive bacterial proteins. Protein & Peptide Letters, 16, 1478-1484. Gpos-mPLoc web server at http://www.csbio.sjtu.edu.cn/bioinf/Gpos-multi/. PMID:20001911
134. Madkan, A., Blank, M., Elson, E., Chou, K.C. , Geddis, M.S., Goodman, R. (2009) Steps to the clinic with ELF EMF. Natural Science (Openly accessible at http://www.scirp.org/journal/NS/), 1, 157-165. doi:doi:10.4236/ns.2009.13020
135. Huang, R. B., Du, Q. S., Wang, C. H., Liao, S. M. & Chou, K.C. (2010). A fast and accurate method for predicting pKa of residues in proteins. Protein Engineering, Design & Selection, 23, 35-42. doi:10.1093/protein/gzp067
136. Zhu, L., Yang, J., Song, J. N., Chou, K.C. and Shen, H. B. (2010). Improving the accuracy of predicting disulfide connectivity by feature selection. Journal of Computational Chemistry, 31, 1478-1485. PMID:20127740
137. Wang, J. F., Wei, D. Q. and Chou, K.C. (2009). Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem Biophys Res Commun 388, 413-417. doi:10.1016/j.bbrc.2009.08.026
138. Lin, W.Z., Xiao, X. & Chou, K.C. (2009). GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis. Protein Eng Des Sel, 22, 699-705. GPCR-GIA web server at http://icpr.jci.jx.cn/bioinfo/GPCR-GIA. doi:10.1093/protein/gzp057
139. Chou, K.C. , Wei, D. Q., Du, Q. S., Sirois, S., Shen, H. B. & Zhong, W. Z. (2009). Study of inhibitors against SARS coronavirus by computational approaches. In Proteases in Biology and Disease (Lendeckel, U. & Hooper, N.M., eds.), in Proteases in Biology and Disease: Viral Proteases and Antiviral Protease Inhibitor Therapy, Vol.8, pp.1-23, Springer Science, Media B.V.
140. Chou, K.C. & Shen, H. B. (2009). FoldRate: A web-server for predicting protein folding rates from primary sequence. The Open Bioinformatics Journal 3, 31-50 (open accessible at http://www.bentham.org/open/tobioij/). FoldRate web server at http://www.csbio.sjtu.edu.cn/bioinf/FoldRate/. doi:10.2174/1875036200903010031
141. Shen, H. B., Song, J. N. & Chou, K.C. (2009). Prediction of protein folding rates from primary sequence by fusing multiple sequential features. Journal of Biomedical Science and Engineering (JBiSE) 2, 136-143 (open accessible at http://www.srpublishing.org/journal/jbise/). Pred-PFR web server at http://www.csbio.sjtu.edu.cn/bioinf/FoldingRate/. doi:10.4236/jbise.2009.23024
142. Wang, S. Q., Du, Q. S., Huang, R. B., Zhang, D. W. & Chou, K.C. (2009). Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus. Biochem Biophys Res Commun 386, 432-436. doi:10.1016/j.bbrc.2009.06.016
143. Shen, H. B. & Chou, K.C. (2009). QuatIdent: A web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information. Journal of Proteome Research, 8, 1577-1584. QuatIdent web server available at http://www.csbio.sjtu.edu.cn/bioinf/Quaternary/. doi:10.1021/pr800957q
144. Du, Q.S., Huang, R.B., Wang, C.H., Li, X.M., & Chou, K.C. (2009). Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus. Journal of Theoretical Biology, 259, 159-164. doi:10.1016/j.jtbi.2009.03.003
145. Shen, H.B. and Chou, K.C. (2009) Identification of proteases and their types. Analytical Biochemistry, 385, 153-160. doi:10.1016/j.ab.2008.10.020
146. Wang, J. F., Zhang, C. C., Yan, J. Y., Chou, K. C. & Wei, D.Q. (2009). Molecular modeling of CYP proteins and its implication for personal drug design. In Automation in Proteomics and Genomics: An Engineering Case-Based Approach (for Harvard/MIT interdisciplinary special studies courses), Chap.11, pp.275-292. (Alterovitz, G., Benson, R., and Ramoni, M.F. ed.), John Wiley & Sons Ltd., West Sussex, UK.
147. Shen, H. B., Wang, J. F., Yao, L. X., Yang, J. & Chou, K. C. (2009). Recent progress of bioinformatics in membrane protein structural studies. In Automation in Proteomics and Genomics: An Engineering Case-Based Approach (for Harvard/MIT interdisciplinary special studies courses), Chap.12, pp.293-308. (Alterovitz, G., Benson, R., and Ramoni, M.F. ed.), John Wiley & Sons Ltd., West Sussex, UK.
148. Wei, H., Wang, C.H., Du, Q.S., Meng, J. & Chou, K.C. (2009). Investigation into Adamantane-Based M2 Inhibitors with FB-QSAR. Medicinal Chemistry, 5, 305-317. PMID:19689387
149. Wang, J. F., Gong, K., Wei, D. Q., Li, Y. X. & Chou, K.C. (2009). Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate binding site to the second one. Protein Engineering Design and Selection 22, 349-355. doi:10.1093/protein/gzp012
150. Xiao, X., Wang, P. & Chou, K.C. (2009). Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition. Journal of Applied Crystallography, 42, 169-173. PQSA-Pred web server at http://icpr.jci.jx.cn/bioinfo/pqsa-pred. doi:10.1107/S0021889809002751
151. Wang J. F., Zhang C. C., Chou, K.C. , Wei D.Q. (2009) Review: Structure of cytochrome P450s and personalized drug. Current Medicinal Chemistry, 16, 232-244. doi:10.2174/092986709787002727
152. Gong, K., Li, L., Wang, J. F., Cheng, F., Wei, D. Q. & Chou, K.C. (2009). Binding mechanism of H5N1 influenza virus neuraminidase with ligands and its implication for drug design. Medicinal Chemistry, 5, 242-249. doi:10.2174/157340609788185936
153. Gu, R. X., Gu, H., Xie, Z. Y., Wang, J. F., Arias, H. R., Wei, D. Q. & Chou, K.C. (2009). Possible drug candidates for Alzheimer's disease deduced from studying their binding interactions with alpha7 nicotinic acetylcholine receptor. Medicinal Chemistry, 5, 250-262. doi:10.2174/157340609788185909
154. Wang, J.F., Yan, J.Y., Wei, D.Q., & Chou, K.C. (2009). Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism. Medicinal Chemistry 5, 263-270. doi:10.2174/157340609788185954
155. Ding, Y. S., Zhang, T. L., Gu, Q., Zhao, P. Y. & Chou, K.C. (2009). Using maximum entropy model to predict protein secondary structure with single sequence. Protein & Peptide Letters, 16, 552-560. doi:10.2174/092986609788167833
156. Prado-Prado, F. J., de la Vega, O. M., Uriarte, E., Ubeira, F. M., Chou, K.C. & Gonzalez-Diaz, H. (2009). Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks. Bioorg Med Chem, 17, 569-575. doi:10.1016/j.bmc.2008.11.075
157. Du, Q. S., Huang, R. B., Wei, Y. T., Pang, Z. W., Du, L. Q. & Chou, K.C. (2009). Fragment-Based Quantitative Structure-Activity Relationship (FB-QSAR) for Fragment-Based Drug Design. Journal of Computational Chemistry, 30, 295-304. doi:10.1002/jcc.21056
158. Huang, R. B., Du, Q. S., Wei, Y. T., Pang, Z. W., Wei, H. & Chou, K.C. (2009). Physics and chemistry-driven artificial neural network for predicting bioactivity of peptides and proteins and their design. Journal of Theoretical Biology, 256, 428-435. doi:10.1016/j.jtbi.2008.08.028
159. Wang, J. F., Wei, D. Q., Du, H. L., Li, Y. X. & Chou, K.C. (2009). Molecular modeling studies on NADP-dependence of Candida tropicalis strain xylose reductase. The Open Bioinformatics Journal, 2, 72-79. doi:10.2174/1875036200802010072
160. Shen, H.B. and Chou, K.C. (2009) Predicting protein fold pattern with functional domain and sequential evolution information. Journal of Theoretical Biology, 256, 441-446. doi:10.1016/j.jtbi.2008.10.007
161. Cruz-Monteagudo, M., Munteanu, C. R., Borges, F., Natália, M., Cordeiro, D. S., Uriarte, E., Chou, K.C. & Gonzalez-Diaz, H. (2008). Stochastic molecular descriptors for polymers. 4. Study of complex mixtures with topological indices of mass spectra spiral and star networks: the blood proteome case. Polymer 49, 5575-5587. doi:10.1016/j.polymer.2008.09.070
162. Shen, H. B. & Chou, K.C. (2008). HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins. Analytical Biochemistry, 375, 388-390. HIVcleave web server at http://chou.med.harvard.edu/bioinf/HIV/. doi:10.1016/j.ab.2008.01.012
163. Shen, H. B. & Chou, K.C. (2008). PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition. Analytical Biochemistry. 373, 386-388. PseAAC web server at http://chou.med.harvard.edu/bioinf/PseAAC/. doi:10.1016/j.ab.2007.10.012
164. Yang, Z. R. & Chou, K.C. (2008). Correlation of metabolic pathways with the primary structure in acetylated proteins. The Open Bioinformatics Journal, 2, 90-96. doi:10.2174/1875036200802010090
165. Shen, H. B., Yi, D. L., Yao, L. X., Yang, J. & Chou, K.C. (2008). Knowledge-based computational intelligence development for predicting protein secondary structures from sequences. Expert Rev Proteomics 5, 653-662. doi:10.1586/14789450.5.5.653
166. Aguero-Chapin G., Antunes A., Ubeira F.M., Chou, K.C. , Gonzalez-Diaz H. (2008) Comparative Study of Topological Indices of Macro/Supra-molecular RNA Complex Networks. Journal of Chemical Information & Modeling, 48, 2265-2277. doi:10.1021/ci8001809
167. Dea-Ayuela M. A., Perez-Castillo Y., Meneses-Marcel A., Ubeira F. M., Bolas-Fernandez F., Chou, K.C. , Gonzalez-Diaz H. (2008) HP-Lattice QSAR for dynein proteins: Experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. Bioorg Med Chem 16, 7770-7776. doi:10.1016/j.bmc.2008.07.023
168. Prado-Prado, F. J., Gonzalez-Diaz, H., de la Vega, O. M., Ubeira, F. M. & Chou, K.C. (2008). Unified QSAR approach to antimicrobials. Part 3: First multi-tasking QSAR model for Input-Coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. Bioorganic & Medicinal Chemistry 16, 5871-5880. doi:10.1016/j.bmc.2008.04.068
169. Xiao, X., Wang, P. & Chou, K.C. (2008). Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image. Journal of Theoretical Biology, 254, 691-696. doi:10.1016/j.jtbi.2008.06.016
170. Wang, T., Yang, J., Shen, H. B. & Chou, K.C. (2008). Predicting membrane protein types by the LLDA algorithm. Protein & Peptide Letters, 15, 915-921. doi:10.2174/092986608785849308
171. Wang, J. F., Wei, D. Q., Li, L. & Chou, K.C. (2008). Review: Pharmacogenomics and personalized use of drugs. Current Topics of Medicinal Chemistry, 8, 1573-1579. doi:10.2174/156802608786786534
172. Wang, J. F., Wei, D. Q., Li, L. & Chou, K.C. (2008). Review: Drug candidates from traditional Chinese medicines. Current Topics of Medicinal Chemistry, 8, 1656-1665. doi:10.2174/156802608786786633
173. Du, Q. S., Huang, R. B. & Chou, K.C. (2008). Review: Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design. Current Protein and Peptide Science, 9, 248-259. doi:10.2174/138920308784534005
174. Xiao, X., Lin, W. Z. & Chou, K.C. (2008). Using grey dynamic modeling and pseudo amino acid components to predict protein structural classes. Journal of Computational Chemistry, 29, 2018-2024. doi:10.1002/jcc.20955
175. Wang, J. F., Wei, D. Q., Chen, C., Li, Y. & Chou, K.C. (2008). Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. Protein & Peptide Letters, 15, 27-32. doi:10.2174/092986608783330305
176. Du, Q. S., Huang, R. B., Wei, Y. T., Du, L. Q. & Chou, K.C. (2008). Multiple Field Three Dimensional Quantitative Structure-Activity Relationship (MF-3D-QSAR). Journal of Computational Chemistry, 29, 211-219. doi:10.1002/jcc.20776
177. Zhang, T. L., Ding, Y. S. & Chou, K.C. (2008). Prediction protein structural classes with pseudo amino acid composition: approximate entropy and hydrophobicity pattern. Journal of Theoretical Biology, 250, 186-193. doi:10.1016/j.jtbi.2007.09.014
178. Shen, H. B. & Chou, K.C. (2007). EzyPred: A top-down approach for predicting enzyme functional classes and subclasses. Biochem Biophys Res Comm, 364, 53-59. EzyPred web server at http://chou.med.harvard.edu/bioinf/EzyPred/. doi:10.1016/j.bbrc.2007.09.098
179. Shen, H. B. & Chou, K.C. (2007). Signal-3L: a 3-layer approach for predicting signal peptide. Biochem Biophys Res Comm, 363, 297-303. doi:10.1016/j.bbrc.2007.08.140
180. Wang, S.Q., Du, Q. S. & Chou, K.C. (2007). Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem Biophys Res Comm, 354, 634-640. doi:10.1016/j.bbrc.2006.12.235
181. Shen, H. B. & Chou, K.C. (2007). Nuc-PLoc: A new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Engineering, Design & Selection, 20, 561-567. Nuc-PLoc web server at http://chou.med.harvard.edu/bioinf/Nuc-PLoc/. doi:10.1093/protein/gzm057
182. Sirois, S., Touaibia, M., Chou, K.C. & Roy, R. (2007). Glycosylation of HIV-1 gp120 V3 loop: towards the rational design of a synthetic carbohydrate vaccine. Current Medicinal Chemistry, 14, 3232-3242. PMID:18220757
183. Guo, X. L., Li, L., Wei, D. Q., Zhu, Y. S. & Chou, K.C. (2007). Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids, 35, 375-382. doi:10.1007/s00726-007-0611-3
184. Du, Q. S., Wang, S. Q. & Chou, K.C. (2007). Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem Biophys Res Comm 362, 525-531. doi:10.1016/j.bbrc.2007.08.025
185. Shen, H. B., Yang, J. & Chou, K.C. (2007). Review: Methodology development for predicting subcellular localization of proteins and their other attributes. Expert Review of Proteomics, 4, 453-464. doi:10.1586/14789450.4.4.453
186. Xiao, X. & Chou, K.C. (2007) Digital coding of amino acids based on hydrophobic index. Protein & Peptide Letters, 14, 871-875. doi:10.2174/092986607782110293
187. Ding, Y. S., Zhang, T. L. & Chou, K.C. (2007). Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein & Peptide Letters, 14, 811-815. doi:10.2174/092986607781483778
188. Zhang, S. W., Zhang, Y. L., Pan, Q., Cheng, Y. M. & Chou, K.C. (2008). Estimating residue evolutionary conservation by introducing von Neumann entropy and a novel gap-treating approach, Amino Acids, 35, 495-501. doi:10.1007/s00726-007-0586-0
189. Shen, H. B. & Chou, K.C. (2007). Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. Biochem Biophys Res Comm, 355, 1006-1011. Hum-mPLoc web server at http://chou.med.harvard.edu/bioinf/hum-multi/. doi:10.1016/j.bbrc.2007.02.071
190. Wang, J. F., Wei, D. Q., Lin, Y., Wang, Y. H., Du, H. L., Li, Y.X. & Chou, K.C. (2007). Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem Biophys Res Comm, 359, 323-329. doi:10.1016/j.bbrc.2007.05.101
191. Li, L., Wei, D. Q., Wang, J. F. & Chou, K.C. (2007). Computational studies of the binding mechanism of calmodulin with chrysin. Biochem Biophys Res Comm, 358, 1102-1107. doi:10.1016/j.bbrc.2007.05.053
192. Li, Y., Wei, D. Q., Gao, W. N., Gao, H., Liu, B. N., Huang, C. J., Xu, W. R., Liu, D. K., Chen, H. F. & Chou, K.C. (2007). Computational approach to drug design for oxazolidinones as antibacterial agents. Medicinal Chemistry, 3, 576-582. doi:10.2174/157340607782360362
193. Wang, J. F., Wei, D. Q., Li, L., Zheng, S. Y. & Chou, K.C. (2007). 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem Biophys Res Comm, 355, 513-519. doi:10.1016/j.bbrc.2007.01.185
194. Du, Q. S., Wei, Y. T., Pang, Z. W., Chou, K.C. & Huang, R. B. (2007). Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction. Protein Engineering, Design & Selection, 20, 417-423. doi:10.1093/protein/gzm036
195. Du, Q. S., Huang, R. B., Wei, Y. T., Wang, C. H. & Chou, K.C. (2007). Peptide reagent design based on physical and chemical properties of amino acid residues. Journal of Computational Chemistry, 28, 2043-2050. doi:10.1002/jcc.20732
196. Shen, H. B. & Chou, K.C. (2007). Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. Protein Engineering, Design, and Selection, 20, 39-46. Gpos-PLoc web server at http://chou.med.harvard.edu/bioinf/Gpos/. doi:10.1093/protein/gzl053
197. Liu, H., Yang, J., Liu, D. Q., Shen, H. B. & Chou, K.C. (2007). Using a new alignment kernel function to identify secretory proteins. Protein & Peptide Letters, 14, 203-208. doi:10.2174/092986607779816087
198. Du, Q. S., Sun, H. & Chou, K.C. (2007). Inhibitor design for SARS coronavirus main protease based on “distorted key theory”. Medicinal Chemistry, 3, 1-6. doi:10.2174/157340607779317616
199. Chen, J., Liu, H., Yang, J. & Chou, K.C. (2007). Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids, 33, 423-428. doi:10.1007/s00726-006-0485-9
200. Zheng, H., Wei, D. Q., Zhang, R., Wang, C., Wei, H. & Chou, K.C. (2007). Screening for New Agonists against Alzheimer's Disease. Medicinal Chemistry, 3, 488-493. doi:10.2174/157340607781745492
201. Shen H.B, Yan J. & Chou, K.C. (2007). Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction. Amino Acids, 33, 57-67. doi:10.1007/s00726-006-0478-8
202. Chou, K.C. & Shen, H.B. (2007). Large-scale plant protein subcellular location prediction. Journal of Cellular Biochemistry, 100, 665-678. Plant-PLoc web server at http://chou.med.harvard.edu/bioinf/plant/. doi:10.1002/jcb.21096
203. Liu, D. Q., Liu, H., Shen, H. B., Yang, J. & Chou, K.C. (2007). Predicting secretory protein signal sequence cleavage sites by fusing the marks of global alignments. Amino Acids, 32, 493-496. doi:10.1007/s00726-006-0466-z
204. Wei, H., Zhang, R., Wang, C., Zheng, H., Chou, K.C. & Wei, D. Q. (2007). Molecular insights of SAH enzyme catalysis and their implication for inhibitor design. Journal of Theoretical Biology, 244, 692-702. doi:10.1016/j.jtbi.2006.09.011
205. Gao, W. N., Wei, D. Q., Li, Y., Gao, H., Xu, W. R., Li, A. X. & Chou, K.C. (2007). Agaritine and its derivatives are potential inhibitors against HIV proteases. Medicinal Chemistry, 3, 221-226. doi:10.2174/157340607780620644
206. Shen, H. B. & Chou, K.C. (2007). Using ensemble classifier to identify membrane protein types. Amino Acids, 32, 483-488. doi:10.1007/s00726-006-0439-2
207. Wang, S. Q., Du, Q. S., Zhao, K., Li, A. X., Wei, D. Q. and Chou, K.C. (2007). Virtual screening for finding natural inhibitor against cathepsin-L for SARS therapy. Amino Acids, 33, 129-135. doi:10.1007/s00726-006-0403-1
208. Wei, D. Q., Du, Q. S., Sun, H. and Chou, K.C. (2006). Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Biochem Biophys Res Comm, 344, 1048-1055. doi:10.1016/j.bbrc.2006.03.210
209. Chou, K.C. & Shen, H. B. (2006). Large-scale predictions of Gram-negative bacterial protein subcellular locations. Journal of Proteome Research, 5, 3420-3428. Gneg-PLoc web server at http://chou.med.harvard.edu/bioinf/Gneg/. doi:10.1021/pr060404b
210. Chou, K.C. , Wei, D.Q., Du, Q.S., Sirois, S., Zhong, W.Z. (2006). Review: Progress in computational approach to drug development against SARS. Current Medicinal Chemistry, 13, 3263-3270. doi:10.2174/092986706778773077
211. Shen, H. B. & Chou, K.C. (2006). Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells. Biopolymers, 85, 233-240. Virus-PLoc web server at http://chou.med.harvard.edu/bioinf/virus/. doi:10.1002/bip.20640
212. Chou, K.C. and Shen, H. B. (2006). Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-nearest neighbor classifiers. Journal of Proteome Research, 5, 1888-1897. Euk-OET-PLoc web server at http://chou.med.harvard.edu/bioinf/euk-oet/. doi:10.1021/pr060167c
213. Chou, K.C. and Shen, H. B. (2006). Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization. Biochem. Biophys. Res. Commun., 347, 150-157. Hum-PLoc web server at http://chou.med.harvard.edu/bioinf/hum/. doi:10.1016/j.bbrc.2006.06.059
214. Shen, H. B. & Chou, K.C. (2006). Ensemble classifier for protein folding pattern recognition. Bioinformatics, 22, 1717-1722. PFP-Pred web server at http://www.csbio.sjtu.edu.cn/bioinf/PFP-Pred/. doi:10.1093/bioinformatics/btl170
215. Wang, S.Q., Yang, J., and Chou, K.C. (2006). Using stacked generalization to predict membrane protein types based on pseudo amino acid composition. Journal of Theoretical Biology, 242, 941-946. doi:10.1016/j.jtbi.2006.05.006
216. Chou, K.C. (2006). Structural bioinformatics and its impact to biomedical science and drug discovery. In Frontiers in Medicinal Chemistry (Atta-ur-Rahman & Reitz, A. B., eds.), Vol. 3, pp. 455-502. Bentham Science Publishers, The Netherlands.
217. Zhang, T., Ding, Y. & Chou, K.C. (2006). Prediction of protein subcellular location using hydrophobic patterns of amino acid sequence. Computational Biology and Chemistry, 30, 367-371. doi:10.1016/j.compbiolchem.2006.08.003
218. Chou, K.C. , Cai, Y.D. and Zhong, W.Z. (2006). Predicting networking couples for metabolic pathways of arabidopsis, EXCLI Journal, 5, 55-65. Openly accessible at www.excli.de/vol5/Chou07-06proofrev.pdf
219. Chou, K.C. & Shen, H. B. (2006). Predicting protein subcellular location by fusing multiple classifiers. Journal of Cellular Biochemistry, 99, 517-527. doi:10.1002/jcb.20879
220. Kem, W., Soti, F., LeFrancois, S., Wildeboer, K., MacDougall, K., Wei, D. Q., Chou, K.C. and Arias, H. R. (2006). Review: The nemertine toxin anabaseine and its derivative DMXBA (GTS-21): chemical and pharmacological properties. Marine Drugs 4, 255-273. doi:10.3390/md403255
221. Du, Q. S., Jiang, Z. Q., He, W. Z., Li, D. P. and Chou, K.C. (2006). Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction. Journal of Biomolecular Structure and Dynamics,23, 635-640. PMID:16615809
222. Chou, K.C. and Cai, Y. D. (2006). Predicting protein-protein interactions from sequences in a hybridization space. Journal of Proteome Research, 5, 316-322. doi:10.1021/pr050331g
223. Xiao, X., Shao, S. H. and Chou, K.C. (2006). A probability cellular automaton model for hepatitis B viral infections. Biochem. Biophys. Res. Comm., 342, 605-610. doi:10.1016/j.bbrc.2006.01.166
224. Zhang, R., Wei, D. Q., Du, Q. S. and Chou, K.C. (2006). Molecular modeling studies of peptide drug candidates against SARS. Medicinal Chemistry, 2, 309-314. doi:10.2174/157340606776930736
225. Bai, Y., Wang, D., Yu, Z. X., Jia, Y., Zhu, F. Y., Wei, D. Q., Zhong, W. Z. and Chou, K.C. (2006). Ecdysterone determination of niuxi by the near-infrared diffuse reflection spectroscopy (NIRDRS). Spectroscopy, 21, 40-43.
226. Chou, K.C. and Cai, Y.D. (2006) Prediction of protease types in a hybridization space, Biochem. Biophys. Res. Comm., 339, 1015-1020. doi:10.1016/j.bbrc.2005.10.196
227. Cai, Y.D. and Chou, K.C. (2006). Predicting membrane protein type by functional domain composition and pseudo amino acid composition. Journal of Theoretical Biology, 238, 395-400. doi:10.1016/j.jtbi.2005.05.035
228. Cai, Y.D., Feng, K.Y., Lu, W.C. and Chou, K.C. (2006). Using LogitBoost classifier to predict protein structural classes. Journal of Theoretical Biology, 238, 172-176. doi:10.1016/j.jtbi.2005.05.034
229. Du, Q.S., Li, D.P., He, W.Z. and Chou, K.C. (2006). Heuristic molecular lipophilicity potential (HMLP): lipophilicity and hydrophilicity of amino acid side chains. Journal of Computational Chemistry, 27, 685-692. doi:10.1002/jcc.20369
230. Niu, B., Cai, Y. D., Lu, W. C., Zheng, G. Y. and Chou, K.C. (2006). Predicting protein structural class with AdaBoost learner. Protein and Peptide Letters, 13, 489-492. doi:10.2174/092986606776819619
231. Gao, L., Ding, Y.S., Dai, H., Shao, S.H., Huang, Z.D., and Chou, K.C. (2006). A novel fingerprint map for detecting SARS-CoV. Journal of Phamaceutical and Biomedical Analysis, 41, 246-250. doi:10.1016/j.jpba.2005.09.031
232. Wei, D. Q., Zhang, R., Du, Q. S., Gao, W. N., Li, Y., Gao, H., Wang, S. Q., Zhang, X., Li, A. X., Sirois, S. and Chou, K.C. (2006). Anti-SARS drug screening by molecular docking. Amino Acids, 31, 73-80. doi:10.1007/s00726-006-0361-7
233. Xiao, X., Shao, S. H., Huang, Z. D. and Chou, K.C. (2006). Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor. Journal of Computational Chemistry, 27, 478-482. doi:10.1002/jcc.20354
234. Xiao, X., Shao, S. H., Ding, Y. S., Huang, Z. D. and Chou, K.C. (2006). Using cellular automata images and pseudo amino acid composition to predict protein sub-cellular location. Amino Acids, 30, 49-54. doi:10.1007/s00726-005-0225-6
235. Wei, D.Q., Sirois, S., Du, Q.S., Arias, H.R., and Chou, K.C. (2005). Theoretical Studies of Alzheimer's Disease Drug Candidate [3-(2,4-Dimethoxy)benzylidene]-anabaseine dihydrochloride (GTS-21) and its derivatives. Biochem. Biophys. Res. Commun., 338, 1059-1064. doi:10.1016/j.bbrc.2005.10.047
236. Liu, H., Yang, J., Ling, J.G., and Chou, K.C. (2005). Prediction of protein signal sequences and their cleavage sites by statistical rulers. Biochem. Biophys. Res. Commun., 338, 1005-1011. doi:10.1016/j.bbrc.2005.10.047
237. Shen, H. B. and Chou, K.C. (2005). Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition. Biochem. Biophys. Res. Comm., 337, 752-756. doi:10.1016/j.bbrc.2005.09.117
238. Liu, H., Wang, M. and Chou, K.C. (2005). Low-frequency Fourier spectrum for predicting membrane protein types. Biochem Biophys Res Commun 336, 737-739. doi:10.1016/j.bbrc.2005.08.160
239. Suzanne, S., Sing, T. and Chou, K.C. (2005). Review: HIV-1 V3 loop for structure-based drug design. Current Protein and Peptide Science, 6, 413-422. PMID:16248793
240. Feng, K.Y., Cai, Y.D. and Chou, K.C. (2005). Boosting classifier for predicting protein domain structural class. Biochemical and Biophysical Research Communications, 334, 213-217. doi:10.1016/j.bbrc.2005.06.075
241. Chou, K.C. (2005). Review: Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Current Protein and Peptide Science, 6, 423-436. PMID:16248794
242. Liu, H., Yang, J., Wang, M., Xue, L. and Chou, K.C. (2005). Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types. The Protein Journal, 24, 385-389. doi:10.1007/s10930-005-7592-4
243. Shi, T. L., Li, Y. X., Cai, Y. D. and Chou, K.C. (2005). Review: Computational methods for protein - protein interaction and their application. Current Protein and Peptide Science, 6, 443-449. PMID:16248796
244. Shen, H.P. and Chou, K.C. (2005). Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo amino acid composition to predict membrane protein types. Biochemical and Biophysical Research Communications, 334, 288-292. doi:10.1016/j.bbrc.2005.06.087
245. Yang, Z. R., Wang, L., Young, N. and Chou, K.C. (2005). Review: Pattern recognition methods for protein functional site prediction. Current Protein and Peptide Science, 6, 479-491. PMID:16248799
246. Shen, H.P., Yang, J., Liu, X.J. and Chou, K.C. (2005). Using supervised fuzzy clustering to predict protein structural classes. Biochemical and Biophysical Research Communications, 334, 577-581. doi:10.1016/j.bbrc.2005.06.128
247. Chou, K.C. (2005). Prediction of G-protein-coupled receptor classes. Journal of Proteome Research, 4, 1413-1418. doi:10.1021/pr050087t
248. Chou, K.C. (2005) Modeling the tertiary structure of human Cathepsin-E, Biochem. Biophys. Res. Commun., 331, 56-60. doi:10.1016/j.bbrc.2005.03.123
249. Gao, Y., Shao, S. H., Xiao, X., Ding, Y. S., Huang, Y. S., Huang, Z. D. and Chou, K.C. (2005). Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter. Amino Acids, 28, 373-376. doi:10.1007/s00726-005-0206-9
250. Cai, Y.D. and Chou, K.C. (2005) Predicting enzyme subclass by functional domain composition and pseudo amino acid composition, Journal of Proteome Research, 4, 967-971. doi:10.1021/pr0500399
251. Chou, K.C. and Cai, Y.D. (2005) Prediction of membrane protein types by incorporating amphipathic effects, Journal of Chemical Information and Modeling, 45, 407-413. doi:10.1021/ci049686v
252. Wang, M., Yang, J. and Chou, K.C. (2005) Using string kernel to predict signal peptide cleavage site based on subsite coupling model, Amino Acids, 28, 395-402. doi:10.1007/s00726-005-0189-6
253. Xiao, X., Shao, S., Ding, Y., Huang, Z., Chen, X. and Chou, K.C. (2005). An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation, Journal of Theoretical Biology, 235, 555-565. doi:10.1016/j.jtbi.2005.02.008
254. Chou, K.C. and Cai, Y.D. (2005) Using GO-PseAA predictor to identify membrane proteins and their types, Biochem. Biophys. Res. Comm., 327, 845-847. doi:10.1016/j.bbrc.2004.12.069
255. Chou, K.C. and Cai, Y.D. (2005) Predicting protein localization in budding yeast. Bioinformatics, 21, 944-950. doi:10.1093/bioinformatics/bti104
256. Xiao, X., Shao, S., Ding, Y., Huang, Z., Huang, Y., and Chou, K.C. (2005) Using complexity measure factor to predict protein subcellular location, Amino Acids, 28, 57-61. doi:10.1007/s00726-004-0148-7
257. Xiao, X., Shao, S., Ding, Y., Huang, Z., Chen, X., and Chou, K.C. (2005) Using cellular automata to generate image representation for biological sequences, Amino Acids, 28, 29-35. doi:10.1007/s00726-004-0154-9
258. Cai, Y.D., Zhou, G.P., and Chou, K.C. (2005) Predicting enzyme family classes by hybridizing gene product composition and pseudo-amino acid composition, Journal of Theoretical Biology, 234, 145-149. doi:10.1016/j.jtbi.2004.11.017
259. Du, Q.S., Wang, S.Q., Jiang, Z.Q., Gao, W.N., Li, Y., Wei, D.Q., and Chou, K.C. (2005) Application of bioinformatics in search for cleavable peptides of SARS-CoV Mpro and chemical modification of octapeptides, Medicinal Chemistry, 1, 209-213. doi:10.2174/1573406053765468
260. Du, Q.S., Mezey, P.G., and Chou, K.C. (2005) Heuristic molecular lipophilicity potential (HMLP): a 2D-QSAR study to LADH of molecular family pyrazole and derivatives, Journal of Computational Chemistry, 26, 461-470. doi:10.1002/jcc.20174
261. Wang, M., Yao, J.S., Huang, Z.D., Xu, Z.J., Liu, G.P., Zhao, H.Y., Wang, X.Y., Yang, J., Zhu, Y.S. and Chou, K.C. (2005). A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis. Medicinal Chemistry, 1, 39-47. doi:10.2174/1573406053402505
262. Sirois, S., Tsoukas, G.M., Chou, K.C. , Wei, D.Q., Boucher, C. and Hatzakis, G.E. (2005) Selection of molecular descriptors with artificial intelligence for the understanding of HIV-1 protease peptidomimetic inhibitors-activity. Medicinal Chemistry, 1, 173-184. PMID:16787312
263. Cai, Y.D. and Chou, K.C. (2005) Using functional domain composition to predict enzyme family classes. Journal of Proteome Research, 4, 109-111. doi:10.1021/pr049835p
264. Du, Q.S., Wang, S., Wei, D.Q., Sirois, S., and Chou, K.C. (2005) Molecular modelling and chemical modification for finding peptide inhibitor against SARS CoV Mpro, Analytical Biochemistry, 337, 262-270. doi:10.1016/j.ab.2004.10.003
265. Sirois, S., Hatzakis, G.E., Wei, D.Q., Du, Q., Chou, K.C. (2005) Assessment of chemical libraries for their druggability, Computational Biology and Chemistry, 29, 55-67. doi:10.1016/j.compbiolchem.2004.11.003
266. Chou, K.C. and Cai, Y.D. (2004) Predicting protein structural class by functional domain composition. Biochem. Biophys. Res. Comm., 321, 1007-1009. doi:10.1016/j.bbrc.2004.07.059
267. Chou, K.C. and Cai, Y.D. (2004) Using GO-PseAA predictor to predict enzyme subclass, Biochem. Biophys. Res. Comm., 325, 506-509. doi:10.1016/j.bbrc.2004.10.058
268. Cai, Y.D. and Chou, K.C. (2004) Predicting 22 protein localizations in budding yeast, Biochem. Biophys. Res. Comm., 323, 425-428. doi:10.1016/j.bbrc.2004.08.113
269. Chou, K.C. and Cai, Y.D. (2004) Predicting enzyme family class in a hybridization space, Protein Science, 13, 2857-2863. doi:10.1110/ps.04981104
270. Wang, M., Yang, J., Xu, Z.J, and Chou, K.C. (2004) SLLE for predicting membrane protein types, Journal of Theoretical Biology, 232, 7-15. doi:10.1016/j.jtbi.2004.07.023
271. Wang, M., Yang, J., Liu, G. P., Xu, Z. J., and Chou, K.C. (2004) Weighted-support vector machines for predicting membrane protein types based on pseudo-amino acid composition. Protein Engineering, Design, and Selection, 17, 509-516. doi:10.1093/protein/gzh061
272. Chou, K.C. (2004) Insights from modeling the tertiary structure of human BACE2. Journal of Proteome Research, 3, 1069-1072. doi:10.1021/pr049905s
273. Du, Q.S., Wang, S.Q., Zhu, Y., Wei, D.Q., Guo, H., Sirois, S., and Chou, K.C. (2004). Ployprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide, Peptides, 25, 1857-1864. doi:10.1016/j.peptides.2004.06.018
274. Chou, K.C. and Cai, Y.D. (2004) Prediction of protein subcellular locations by GO-FunD-PseAA predictor. Biochem. Biophys. Res. Comm., 320, 1236-1239. doi:10.1016/j.bbrc.2004.06.073
275. Geng, J.G., Chen, M., and Chou, K.C. (2004) P-selectin cell adhesion molecule in inflammation, thrombosis, cancer growth and metastasis. Current Medicinal Chemistry, 11, 2153-2160. PMID:15279555
276. Chou, K.C. (2004). Insights from modeling three-dimensional structures of the human potassium and sodium channels. Journal of Proteome Research, 3, 856-861. doi:10.1021/pr049931q
277. Chou, K.C. and Cai, Y.D. (2004). Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition. Journal of Cellular Biochemistry, 91, 1197-1203. doi:10.1002/jcb.10790
278. Chou, K.C. and Cai, Y.D. (2004). A novel approach to predict active sites of enzyme molecules, PROTEINS: Structure, Function, and Genetics, 55, 77-82. doi:10.1002/prot.10622
279. Sirois, S., Wei, D.Q., Du, Q., and Chou, K.C. (2004). Virtual screening for SARS-CoV protease based on KZ7088 pharmacophore points, Journal of Chemical Information and Computer Science, 44, 1111-1122. doi:10.1021/ci034270n
280. Cai, Y.D. and Chou, K.C. (2004). Predicting subcellular localization of proteins in a hybridization space, Bioinformatics, 20, 1151-1156. doi:10.1093/bioinformatics/bth054
281. Cai, Y.D., Zhou, G.P., Jen, C.H., Lin, S.L., and Chou, K.C. (2004). Identify catalytic triads of serine hydrolases by support vector machines, Journal of Theoretical Biology, 228, 551-557. doi:10.1016/j.jtbi.2004.02.019
282. Yang, Z.R. and Chou, K.C. (2004). Predicting the linkage sites in glycoproteins using bio-basis function neural network, Bioinformatics, 20, 903-908. doi:10.1093/bioinformatics/bth001
283. Cai, Y.D., Ricardo, P.W., Jen, C.H., and Chou, K.C. (2004). Application of SVM to predict membrane protein types, Journal of Theoretical Biology, 226, 373-376. doi:10.1016/j.jtbi.2003.08.015
284. Yang, Z.R. and Chou, K.C. (2004). Bio-support vector machines for computational proteomics, Bioinformatics, 20, 735-741. doi:10.1093/bioinformatics/btg477
285. Chou, K.C. and Cai, Y.D. (2003). Prediction and classification of protein subcellular location: sequence-order effect and pseudo amino acid composition, Journal of Cellular Biochemistry, 90, 1250-1260. doi:10.1002/jcb.10719
286. Du, Q., Wei, D.Q., and Chou, K.C. (2003). Correlations of amino acids in proteins, Peptides, 24, 1863-1869. doi:10.1016/j.peptides.2003.10.012
287. Yang, Z.R. and Chou, K.C. (2003). Mining biological data using self-organizing map. Journal of Chemical Information and Computer Science, 43, 1748-1753. doi:10.1021/ci034138n
288. Chou, K.C. and Cai, Y.D. (2003). A new hybrid approach to predict subcellular localization of proteins by incorporating gene oncology composition, Biochem. Biophys. Res. Comm. 311, 743-747. doi:10.1016/j.bbrc.2003.10.062
289. Chou, K.C. and Cai, Y.D. (2003). Predicting protein quaternary structure by pseudo amino acid composition. PROTEINS: Structure, Function, and Genetics, 53, 282-289. doi:10.1002/prot.10500
290. Cai, Y.D. and Chou, K.C. (2003). Nearest neighbor algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition, Biochemical and Biophysical Research Communications 305, 407-411. doi:10.1016/S0006-291X(03)00775-7
291. Cai, Y.D., Feng, K.Y., Li, Y.X., and Chou, K.C. (2003). Support vector machine for predicting -turn types, Peptides 24, 629-630. doi:10.1016/S0196-9781(03)00100-1
292. Chou, K.C. and Elrod, D.W. (2003). A bioinformatical analysis of enzyme family classes. Journal of Proteome Research 2, 183-190. doi:10.1021/pr0255710
293. Cai, Y.D., Liu, X.J., Li, Y.X., Xu, X.B., and Chou, K.C. (2003). Prediction of -turns with learning machines, Peptides 24, 665-669. doi:10.1016/S0196-9781(03)00133-5
294. Cai, Y.D., Liu, X.J., Xu, X.B., and Chou, K.C. (2003). Support vector machines for prediction of protein domain structural class. Journal of Theoretical Biology 221, 115-120. doi:10.1006/jtbi.2003.3179
295. Cai, Y.D., Liu, X.J., and Chou, K.C. (2003). Prediction of protein secondary structure content by artificial neural network. Journal of Computational Chemistry 24, 727-731. doi:10.1002/jcc.10222
296. Cai, Y.D., Lin, S.L., and Chou, K.C. (2003). Support vector machines for prediction of protein signal sequences and their cleavage sites. Peptides 24, 159-161. doi:10.1016/S0196-9781(02)00289-9
297. Chou, K.C. and Howe,W.J. (2002). Prediction of the tertiary structure of beta-secretase zymogen. Biochem. and Biophys. Res. Commun. 292, 702-708. doi:10.1006/bbrc.2002.6686
298. Chou, K.C. and Elrod, D.W. (2002). A bioinformatical analysis of G-protein-coupled receptors. Journal of Proteome Research 1, 429-434. doi:10.1021/pr025527k
299. Chou, K.C. (2002). Prediction of protein signal sequences. Current Protein and Peptide Science 3, 615-622. doi:10.2174/1389203023380468
300. Chou, K.C. (2002). A new branch of proteomics: prediction of protein cellular attributes. In Gene Cloning and Expression Technology (Eds. Weiner, M. and Lu, Q.), Eaton Publishing, Chapter 4, 57-70. Eaton Publishing Company, Westborough, MA.
301. Elrod, D.W. and Chou, K.C. (2002). A study on the correlation of G-protein coupled receptor types with amino-acid-composition. Protein Engineering, 15, 713-715. doi:10.1093/protein/15.9.713
302. Cai, Y.D., Hu, J. Liu, X.J., and Chou, K.C. (2002). Prediction of protein structural classes by neural network method. Internet Electronic Journal of Molecular Design 1, 332-338.
303. Cai, Y.D., Liu, X.J., Xu, X.B. and Chou, K.C. (2002). Support vector machines for the classification and prediction of -turn types. Journal of Peptide Science 8, 297-301. doi:10.1002/psc.401
304. Cai, Y.D., Liu, X.J., Xu, X.B. and Chou, K.C. (2002). Artificial neural netwok method for predicting protein secondary structure content. Computers and Chemistry 26, 347-350. doi:10.1016/S0097-8485(01)00125-5
305. Cai, Y.D., Liu, X.J., Xu, X.B. and Chou, K.C. (2002). Prediction of protein structural classes by support vector machines. Computers and Chemistry 26, 293-296. doi:10.1016/S0097-8485(01)00113-9
306. Zhang, J., Luan, C.H., Chou, K.C. and Johnson, G.V.W. (2002). Identification of the N-Terminal Functional Domains of Cdk5 by Molecular Truncation and Computer Modeling. PROTEINS: Structure, Function, and Genetics 48, 447-453. doi:10.1002/prot.10173
307. Cai, Y.D., Liu, X.J., Xu, X.B. and Chou, K.C. (2002). SVM for predicting membrane protein types by incorporating quasi-sequence-order effect. Internet Electronic Journal of Molecular Design 1, 219-226.
308. Cai, Y. D., Liu, X. J., Xu, X. B. and Chou, K.C. (2002). Support vector machines for predicting the specificity of GalNAc-transferase. Peptides 23, 205-208. doi:10.1016/S0196-9781(01)00597-6
309. Cai, Y.D., Liu, X.J., and Chou, K.C. (2002). Artificial neural network model for predicting protein subcellular location. Computers and Chemistry 26, 179-182. doi:10.1016/S0097-8485(01)00106-1
310. Cai, Y. D., Liu, X. J., Xu, X. B. and Chou, K.C. (2002). Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect. Journal of Cellular Biochemistry 84, 343-348. doi:10.1002/jcb.10030
311. Cai, Y. D., Liu, X. J., Xu, X. B. and Chou, K.C. (2002). Support vector machines for predicting HIV protease cleavage sites in proteins. Journal of Computational Chemistry 23, 267-274. doi:10.1002/jcc.10017
312. Chou, K.C. (2001). Prediction of signal peptides using scaled window. Peptides 22, 1973-1979. doi:10.1016/S0196-9781(01)00540-X
313. Chou, K.C. (2001). Using subsite coupling to predict signal peptides. Protein Engineering 14, 75-79. doi:10.1093/protein/14.2.75
314. Cai, Y.D., Liu, X.J. and Chou, K.C. (2001). Artificial neural network model for predicting membrane protein types. Journal of Biomolecular Structure and Dynamics 18, 607-610. PMID:11245255
315. Rank, K.B., Mildner, A.M., Leone, J.W., Koeplinger, K.K., Chou, K.C. , Tomasselli, A. G., Heinikson, R. L. and Sharma, S. K. (2001). [W206R]-protease 3: an inactivatable substrate for caspase 8. Protein Expression and Purification, 22, 258-266. doi:10.1006/prep.2001.1433
316. Chou, K.C. (2000). Prediction of protein structural classes and subcellular locations. Current Protein and Peptide Science, 1, 171-208. doi:10.2174/1389203003381379
317. Chou, K.C. (2000). Prediction of protein signal sequences and their cleavage sites. PROTEINS: Structure, Function, and Genetics 42, 136-139. doi:10.1002/1097-0134(20010101)42:1<136::AID-PROT130>3.0.CO;2-F
318. Chou, K.C. (2000). Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. and Biophys. Res. Commun. 278, 477-483. doi:10.1006/bbrc.2000.3815
319. Cai, Y.D., Li, Y.X. and Chou, K.C. (2000). Using neural networks for prediction of domain structural classes. BBA 1476, 1-2. PMID:10606760
320. Cai, Y.D., Liu, X.J., Xu, X. B. and Chou, K.C. (2000). Support vector machines for prediction of protein subcellular location. Molecular Cell Biology Research Communications 4, 230-233. doi:10.1006/mcbr.2001.0285
321. Cai, Y.D. and Chou, K.C. (2000). Using neural networks for prediction of subcellular location of prokaryotic and eukaryotic proteins. Molecular Cell Biology Research Communications 4, 172-173. doi:10.1006/mcbr.2001.0269
322. Chou, K.C. and Elrod, D.W. (1999). Prediction of membrane protein types and subcellular locations. PROTEINS: Structure, Function, and Genetics 34, 137-153. doi:10.1002/(SICI)1097-0134(19990101)34:1<137::AID-PROT11>3.0.CO;2-O
323. Chou, K.C. (1999). Using pair-coupled amino-acid composition to predict protein secondary structure content. Journal of Protein Chemistry 18, 473-480. doi:10.1023/A:1020696810938
324. Cai, Y. D., Li, Y. X., and Chou, K.C. (1999). Classification and prediction of beta-turn types by neural networks. Advances in Engineering Software, 30, 347-352. doi:10.1016/S0965-9978(98)00090-8
325. Cai, Y. D. and Chou, K.C. (1999). Artificial neural network for predicting alpha-turn types. Analytical Biochemistry 268, 407-409. doi:10.1006/abio.1998.2992
326. Liu, W. and Chou, K.C. (1999). Protein secondary structural content prediction. Protein Engineering 12, 1041-1050. doi:10.1093/protein/12.12.1041
327. Chou, K.C. , Watenpaugh, K.D., and Heinrikson, R.L. (1999). A model of the complex between cyclin-dependent kinase 5 and the activation domain of neuronal cdk5 activator. Biochem. Biophys. Res. Commun. 259, 420-428. doi:10.1006/bbrc.1999.0792
328. Chou, K.C. (1999). A key driving force in determination of protein structural classes. Biochem. Biophys. Res. Commun. 264, 216-224. doi:10.1006/bbrc.1999.1325
329. Chou, K.C. , Liu, W., Maggiora, G.M., and Zhang, C.T. (1998). Prediction and classification of domain structural classes. PROTEINS: Structure, Function, and Genetics 31, 97-103. PMID:9552161
330. Chou, K.C. and Maggiora, G.M. (1998). Domain structural class prediction. Proteins Engineering 11, 523-538. doi:10.1093/protein/11.7.523
331. Chou, K.C. and Elrod, D. W. (1998). Using discriminant function for prediction of subcellular location of prokaryotic proteins. Biochem. Biophys. Res. Commun. 252, 63-68. doi:10.1006/bbrc.1998.9498
332. Carter, D. B. and Chou, K.C. (1998). A model for structure dependent binding of Congo Red to Alzeheimer beta-amyloid fibrils. Neurobiology of Aging 19, 37-40. doi:10.1016/S0197-4580(97)00164-4
333. Cai, Y.D., Yu, H. and Chou, K.C. (1998). Prediction of beta-turns. Journal of Protein Chemistry 17, 363-376. doi:10.1023/A:1022559300504
334. Cai, Y.D. and Chou, K.C. (1998). Artificial neural network model for HIV protease cleavage sites in proteins. Advances in Engineering Software 29, 119-128. doi:10.1016/S0965-9978(98)00046-5
335. Cai, Y.D., Yu, H. and Chou, K.C. (1998). Using neural network for prediction of HIV protease cleavage sites in proteins. Journal of Protein Chemistry 17, 607-615. doi:10.1007/BF02780962
336. Liu, W. and Chou, K.C. (1998). Singular points of protein beta-sheets. Protein Science 7, 2324-2330. doi:10.1002/pro.5560071109
337. Zhang, C.T. and Chou, K.C. (1998). Reply to: Comment on the recent prediction of a microwave beat motion in DNA. Chemical Physics 229, 345-346. doi:10.1016/S0301-0104(98)00003-2
338. Liu, W. and Chou, K.C. (1998). Prediction of protein structural classes by modified Mahalanobis discriminant algorithm. Journal of Protein Chemistry 17, 209-217. doi:10.1023/A:1022576400291
339. Chou, K.C. (1997). Prediction of beta-turns in proteins. Journal of Peptide Research 49, 120-144. doi:10.1111/j.1399-3011.1997.tb00608.x
340. Chou, K.C. and Blinn, J. R. (1997). Classification and prediction of beta-turn types. Journal of Protein Chemistry 16, 575-595. doi:10.1023/A:1026366706677
341. Chou, K.C. and Heinrikson, R. L. (1997). Prediction of the tertiary structure of the complement control protein module. Journal of Protein Chemistry 16, 765-773. doi:10.1023/A:1026363816730
342. Chou, K.C. (1997). Prediction and classification of alpha-turn types. Biopolymers 42, 837-853. doi:10.1002/(SICI)1097-0282(199712)42:7<837::AID-BIP9>3.0.CO;2-U
343. Chou, K.C. , Jones, D. and Heinrikson, R. L. (1997). Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Letters 419, 49-54. PMID:9426218
344. Chou, K.C. , Zhang, C.T., Maggiora and M, G. (1997). Disposition of amphiphilic helices in heteropolar environments. PROTEINS: Structure, Function, and Genetics 28, 99-108. PMID:9144795
345. Zhang, C.T. and Chou, K.C. (1997). Prediction of beta-turns in proteins by 1-4 and 2-3 correlation model. Biopolymers 41, 673-702. doi:10.1002/(SICI)1097-0282(199705)41:6<673::AID-BIP7>3.0.CO;2-N
346. Cai, Y.D., Yu, H. and Chou, K.C. (1997). Artificial neural network method for predicting the specificity of GalNAc-transferase. Journal of Protein Chemistry 16, 689-700. doi:10.1023/A:1026306520790
347. Chou, K.C. , Tomasselli, A.L., Reardon, I.M. and Heinrikson, R.L. (1996). Predicting HIV protease cleavage sites in proteins by a discriminant function method. PROTEINS: Structure, Function, and Genetics 24, 51-72. PMID:8628733
348. Chou, K.C. (1996). Knowledge-based model building of tertiary structures for lectin domains of the selectin family. Journal of Protein Chemistry 15, 161-168. doi:10.1007/BF01887396
349. Chou, K.C. , Zhang, C.T. and Elrod, D.W. (1996). Do antisense proteins exist? Journal of Protein Chemistry 15, 59-61. doi:10.1007/BF01886811
350. Maggiora, G.M., Zhang, C.T., Chou, K.C. and Elrod, D.W. (1996). Combining fuzzy clustering and neural networks to predict protein structural classes. In Neural Networks in QSAR and Drug Design (Devillers, J., ed.), pp. 255-279. Academic Press, London. doi:10.1016/B978-012213815-7/50012-1
351. Cai, Y.D. and Chou, K.C. (1996). Artificial neural network model for predicting specificity of GalNAc-transferase. Analytical Biochemistry 243, 284-285. doi:10.1006/abio.1996.0520
352. Althaus, I.W., Chou, K.C. , Franks, K.M., Diebel, M.R., Kezdy, F.J., Romero, D. L., Thomas, R.C., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1996). The benzylthio-pyrididine U-31,355 is a potent inhibitor of HIV-1 reverse transcriptase. Biochemical Pharmacology 51, 743-750. doi:10.1016/0006-2952(95)02390-9
353. Zhang, C.T. and Chou, K.C. (1996). An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequences. Amino Acids 10, 253-262. doi:10.1007/BF00807327
354. Zhang, C.T. and Chou, K.C. (1996). Beating motion in DNA double helix and a mechanism of energy exchange between its two strands. Chemical Physics 206, 271-277. doi:10.1016/0301-0104(96)00018-3
355. Chou, K.C. , Zhang, C.T., Kezdy, F.J. and Poorman, R.A. (1995). A vector projection method for predicting the specificity of GalNAc-transferase. PROTEINS: Structure, Function, and Genetics 21, 118-126. doi:10.1002/prot.340210205
356. Chou, K.C. (1995) Does the folding type of a protein depend on its amino acid composition? FEBS Letters 363, 127-131. doi:10.1016/0014-5793(95)00245-5
357. Chou, K.C. (1995) A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase. Protein Science 4, 1365-1383. doi:10.1002/pro.5560040712
358. Chou, K.C. (1995) The convergence-divergence duality in lectin domains of the selectin family and its implications. FEBS Letters 363 123-126. doi:10.1016/0014-5793(95)00240-A
359. Zhang, C.T. and Chou, K.C. (1995). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. II. Correlative effect. Journal of Protein Chemistry 14, 251-258. doi:10.1007/BF01886766
360. Zhang, C.T. and Chou, K.C. (1995). An analysis of protein folding type prediction by seed-propagated sampling and jackknife test. Journal of Protein Chemistry 14, 583-593. doi:10.1007/BF01886884
361. Thompson, T.B., Chou, K.C. and Zheng, C. (1995). Neural network prediction of the HIV-1 protease cleavage sites. Journal of Theoretical Biology 177, 369-379. doi:10.1006/jtbi.1995.0254
362. Thompson, T.B., Chou, K.C. and Zheng, C. (1995). What is the origin of the strong electrostatic loop-helix interactions in bundle motif protein structures? Journal of Protein Chemistry 14, 559-566. doi:10.1007/BF01886882
363. Zhang, C.T. and Chou, K.C. (1995). The nonlinear stretching model of hydrogen bonds and local self-fluctuation of base rotation in DNA. Chemical Physics 191, 17-23. doi:10.1016/0301-0104(94)00362-E
364. Zhang, C.T., Chou, K.C. and Maggiora, G.M. (1995). Predicting protein structural classes from amino acid composition: application of fuzzy clustering. Protein Engineering 8, 425-435. doi:10.1093/protein/8.5.425
365. Zhang, C.T. and Chou, K.C. (1995). An eigenvalue-eigenvector approach to predicting protein folding types. Journal of Protein Chemistry 14, 309-326. doi:10.1007/BF01886788
366. Chou, K.C. , Zhang, C.T. and Maggiora, G.M. (1994). Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers 34, 143-153. doi:10.1002/bip.360340114
367. Chou, K.C. , Kezdy, F.J. and Reusser, F. (1994). Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Analytical Biochemistry 221, 217-230. doi:10.1006/abio.1994.1405
368. Chou, K.C. (1994). A molecular piston mechanism of pumping protons by bacteriorhodopsin. Amino Acids 7, 1-17. doi:10.1007/BF00808442
369. Mao, B., Chou, K.C. and Zhang, C.T. (1994). Protein folding classes: a geometric interpretation of the amino acid composition of globular proteins. Protein Engineering 7, 319-330. doi:10.1093/protein/7.3.319
370. Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C. , Kezdy, F. J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1994). Steady-state kinetic studies with the polysulfonate U-9843, an HIV reverse transcriptase inhibitor. Experientia 50, 23-28. doi:10.1007/BF01992044
371. Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C. , Kezdy, F. J., Romero, D.L., Thomas, R.C., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1994). Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-90152E. Biochemical Pharmacology 47, 2017-2028. doi:10.1016/0006-2952(94)90077-9
372. Zhang, C.T. and Chou, K.C. (1994). Analysis of codon usage in 1562 E. Coli protein coding sequences. Journal of Molecular Biology 238, 1-8. doi:10.1006/jmbi.1994.1263
373. Chou, K.C. (1993). Conformational change during photocycle of bacteriorhodopsin and its proton-pumping mechanism. Journal of Protein Chemistry 12, 337-350. doi:10.1007/BF01028196
374. Chou, K.C. , Zhang, C.T. and Kezdy, F.J. (1993). A vector approach to predicting HIV protease cleavage sites in proteins. Proteins: Structure, Function, and Genetics 16, 195-204. doi:10.1002/prot.340160206
375. Chou, K.C. and Zhang, C.T. (1993). Studies on the specificity of HIV protease: an application of Markov chain theory. Journal of Protein Chemistry 12, 709-724. doi:10.1007/BF01024929
376. Chou, K.C. (1993). Prediction of protein folding types from amino acid composition by correlation angles. Amino Acids 6, 231-246. doi:10.1007/BF00813744
377. Chou, K.C. (1993). Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics. Journal of Mathematical Chemistry 12, 97-108. doi:10.1007/BF01164628
378. Chou, K.C. and Zhang, C.T. (1993). A new approach to predicting protein folding types. Journal of Protein Chemistry 12, 169-178. doi:10.1007/BF01026038
379. Zhang, C.T. and Chou, K.C. (1993). An alternate-subsite-coupled model for predicting HIV protease cleavage sites in proteins. Protein Engineering 7, 65-73. doi:10.1093/protein/7.1.65
380. Althaus, I.W., Gonzales, A.J., Chou, J.J., Diebel, M.R., Chou, K.C. , Kezdy, F. J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993). The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. Journal of Biological Chemistry 268, 14875-14880. PMID:7686907
381. Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C. , Kezdy, F. J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993). Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry 32, 6548-6554. doi:10.1021/bi00077a008
382. Althaus, I.W., Chou, J.J., Gonzales, A.J., Diebel, M.R., Chou, K.C. , Kezdy, F. J., Romero, D.L., Aristoff, P.A., Tarpley, W.G. and Reusser, F. (1993). Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. Journal of Biological Chemistry 268, 6119-6124. PMID:7681060
383. Zhang, C.T. and Chou, K.C. (1993). Graphic analysis of codon usage strategy in 1490 human proteins. Journal of Protein Chemistry 12, 329-335. doi:10.1007/BF01028195
384. Chou, K.C. and Zheng, C. (1992). Strong electrostatic loop-helix interactions in bundle motif protein structures. Biophysical Journal 63, 682-688. doi:10.1016/S0006-3495(92)81653-3
385. Chou, K.C. , Carlacci, L., Maggiora, G.M., Parodi, L.A. and Schultz, M. W. (1992). An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin. Protein Science 1, 810-827. doi:10.1002/pro.5560010613
386. Chou, K.C. and Zhang, C.T. (1992). A correlation coefficient method to predicting protein structural classes from amino acid compositions. European Journal of Biochemistry 207, 429-433. doi:10.1111/j.1432-1033.1992.tb17067.x
387. Chou, K.C. and Zhang, C.T. (1992). Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Research and Human Retroviruses 8, 1967-1976. doi:10.1089/aid.1992.8.1967
388. Zhang, C.T. and Chou, K.C. (1992). Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. Biophysical Journal 63, 1523-1529. doi:10.1016/S0006-3495(92)81728-9
389. Blinn, J.R., Chou, K.C. , Howe, W.J., Maggiora, G.M., Mao, B. and Moon, J.B. (1992). Computer Modeling of Constrained Peptide Systems. In Molecular Aspects of Biotechnology: Computational Modes and Theories (Bertran, J., ed.), pp. 17-38. Kluwer Academic Publishers.
390. Zhang, C.T. and Chou, K.C. (1992). An optimization approach to predicting protein structural class from amino acid composition. Protein Science 1, 401-408. doi:10.1002/pro.5560010312
391. Chou, K.C. and Carlacci, L. (1991). Simulated annealing approach to the study of protein structures. Protein Engineering 4, 661-667. doi:10.1093/protein/4.6.661
392. Chou, K.C. (1991). The role of loops in stabilizing bundle motif protein structures. Protein Engineering 4, 849-850. doi:10.1093/protein/4.7.849-a
393. Chou, K.C. and Carlacci, L. (1991). Energetic approach to the folding of alpha/beta barrels. Proteins: Structure, Function, and Genetics 9, 280-295. doi:10.1002/prot.340090406
394. Carlacci, L., Chou, K.C. and Maggiora, G.M. (1991). A heuristic approach to predicting the tertiary structure of bovine somatotropin. Biochemistry 30, 4389-4398. doi:10.1021/bi00232a004
395. Maggiora, G.M., Mao, B., Chou, K.C. and Narasimhan, S.L. (1991). Theoretical and empirical approaches to protein-structure prediction and analysis. In: Methods of Biochemical Analysis, Vol. 23, Chapter 1, pp. 1-86.
396. Carlacci, L. and Chou, K.C. (1991). New development on energetic approach to the packing in proteins. Journal of Computational Chemistry 12, 410-415. doi:10.1002/jcc.540120315
397. Carlacci, L., Schultz, M. and Chou, K.C. (1991). Geometric and energy parameters in lysine-retinal chromophores. Protein Engineering 4, 885-889. doi:10.1093/protein/4.8.885
398. Maggiora, G.M., Mao, B. and Chou, K.C. (1991). Chiral features of proteins. In New Developments in Molecular Chirality (Mezey, P. G., ed.), pp. 93-118. doi:10.1007/978-94-011-3698-3_3
399. Mao, B., Maggiora, G.M. and Chou, K.C. (1991). Mass-weighted molecular dynamics simulation of cyclic polypeptides. Biopolymers 31, 1077-1086. doi:10.1002/bip.360310907
400. Chou, K.C. , Heckel, A., Nemethy, G., Rumsey, S., Carlacci, L. and Scheraga, H. A. (1990). Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins. Proteins: Structure, Function, and Genetics 8, 14-22. doi:10.1002/prot.340080105
401. Carlacci, L. and Chou, K.C. (1990). Monte Carlo method applied in the search for low energy conformations of beta-alpha-beta-alpha-beta structures. Biopolymers 30, 135-150. doi:10.1002/bip.360300114
402. Carlacci, L. and Chou, K.C. (1990). Energetic approach to the folding of four a-helices connected sequentially. Protein Engineering 3, 509-514. doi:10.1093/protein/3.6.509
403. Carlacci, L. and Chou, K.C. (1990). Electrostatic interactions between loops and alpha-helices in 4-helix bundle proteins. Protein Engineering 4, 225-227. doi:10.1093/protein/4.2.225
404. Mao, B., Chou, K.C. and Maggiora, G.M. (1990). Topological analysis of hydrogen bonding in protein structure. European Journal of Biochemistry 188, 361-365. doi:10.1111/j.1432-1033.1990.tb15412.x
405. Maggiora, G.M., Mezey, P.G., Mao, B. and Chou, K.C. (1990). A new chiral feature in alpha-helical domains of proteins. Biopolymers 30, 211-214. doi:10.1002/bip.360300121
406. Chou, K. C., Nemethy, G., Pottle, M. and Scheraga, H.A. (1989). Energy of stabilization of the right-handed alpha-beta-alpha crossover in proteins. Journal of Molecular Biology 205, 241-249. doi:10.1016/0022-2836(89)90378-1
407. Chou, K. C. and Mao, B. (1988). Collective motion in DNA and its role in drug intercalation. Biopolymers 27, 1795-1815. doi:10.1002/bip.360271109
408. Chou, K. C. and Maggiora, G. M. (1988). The biological functions of low-frequency phonons: 7. The impetus for DNA to accommodate intercalators. British Polymer Journal 20, 143-148. doi:10.1002/pi.4980200209
409. Chou, K. C. (1987). The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers 26, 285-295. doi:10.1002/bip.360260209
410. Chou, K. C., Nemethy, G., Rumsey, S., Tuttle, R. W. and Scheraga, H. A. (1986). Interactions between two beta-sheets: Energetics of beta/beta packing in proteins. Journal of Molecular Biology 188, 641-649. doi:10.1016/S0022-2836(86)80012-2
411. Chou, K. C. (1986). Origin of low-frequency motion in biological macromolecules: A view of recent progress of quasi-continuity model. Biophysical Chemistry 25, 105-116. doi:10.1016/0301-4622(86)87001-6
412. Chou, K. C., Nemethy, G., Rumsey, S., Tuttle, R. W. and Scheraga, H. A. (1985). Interactions between an alpha-helix and a beta-sheet: Energetics of alpha/beta packing in proteins. Journal of Molecular Biology 186, 591-609. doi:10.1016/0022-2836(85)90133-0
413. Gerritsen, M., Chou, K. C., Nemethy, G. and Scheraga, H. A. (1985). Energetics of multi-helix interactions in protein folding: Application to myoglobin. Biopolymers 24, 1271-1293. doi:10.1002/bip.360240714
414. Chou, K. C., Nemethy, G., Pottle, M. S. and Scheraga, H. A. (1985). The folding of the twisted beta-sheet in bovine pancreatic trypsin inhibitor. Biochemistry 24, 7948-7953. doi:10.1021/bi00348a016
415. Chou, K. C. and Kiang, Y. S. (1985). The biological functions of low-frequency phonons: 5. A phenomenological theory. Biophysical Chemistry 22, 219-235. doi:10.1016/0301-4622(85)80045-4
416. Chou, K. C. (1985). Low-frequency motions in protein molecules: beta-sheet and beta-barrel. Biophysical Journal 48, 289-297. doi:10.1016/S0006-3495(85)83782-6
417. Chou, K. C. (1985). Prediction of a low-frequency mode in BPTI. International Journal of Biological Macromolecules 7, 77-80. doi:10.1016/0141-8130(85)90035-2
418. Chou, K. C. (1984). The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition. Biophysical Chemistry 20, 61-71. doi:10.1016/0301-4622(84)80005-8
419. Chou, K. C., Nemethy, G. and Scheraga, H. A. (1983). Energetic approach to packing of alpha-helices: 1. Equivalent helices. Journal of Physical Chemistry 87, 2869-2881. doi:10.1021/j100238a033
420. Chou, K. C., Nemethy, G. and Scheraga, H. A. (1983). Effects of amino acid composition on the twist and the relative stability of parallel and antiparallel beta-sheets. Biochemistry 22, 6213-6221. doi:10.1021/bi00295a027
421. Chou, K. C. (1983). Advances in graphical methods of enzyme kinetics. Biophysical Chemistry 17, 51-55. doi:10.1016/0301-4622(83)87013-6
422. Chou, K. C. (1983). Low-frequency vibrations of helical structures in protein molecules. Biochemical Journal 209, 573-580. PMID:6870784
423. Sobell, H.M., Banerjee, A., Lozansky, E.D., Zhou, G.P. and Chou, K.C. (1983). The role of low-frequency (acoustic) phonons in determining the premelting and melting behaviors of DNA. In: Structure and Dynamics: Nucleic Acids and Proteins (Clementi, E. and Sarma, R. H., eds.), pp.181-195. Adenine Press, N.Y.
424. Chou, K. C. (1983). Identification of low-frequency modes in protein molecules. Biochemical Journal 215, 465-469. PMID:6362659
425. Chou, K. C., Pottle, M., Nemethy, G., Ueda, Y. and Scheraga, H. A. (1982). Structure of beta-sheets: Origin of the right-handed twist and of the increased stability of antiparallel over parallel sheets. Journal of Molecular Biology 162, 89-112. doi:10.1016/0022-2836(82)90163-2
426. Scheraga, H. A., Chou, K. C. and Nemethy, G. (1982). Interactions between the fundamental structures of polypeptide chains. In: Conformation in Biology (Srinivasan, R. and Sarma, R. H., eds.), pp.1-10. Adenine Press, Gilderland, NY.
427. Lin, S. X., Chou, K. C. and Wong, J. T. F. (1982). A thermal-variation method for analyzing the rate constants of the Michaelis-Menton mechanism. Biochemical Journal 207, 179-181. PMID:7181857
428. Chou, K. C., Li, T. T. and Zhou, G. Q. (1981). A semi-analytical expression for the concentration distribution of substrate molecules in fast, enzyme-catalyzed reaction systems. Biochimica et Biophysica Acta 657, 304-308. PMID:7213748
429. Chou, K. C., Carter, R. E. and Forsen, S. (1981). A new graphical method for deriving rate equations for complicated mechanisms. Chemica Scripta 18, 82-86.
430. Chou, K. C. (1981). Two new schematic rules for rate laws of enzyme-catalyzed reactions. Journal of Theoretical Biology 89, 581-592. doi:10.1016/0022-5193(81)90030-8
431. Chou, K. C. and Forsen, S. (1981). Graphical rules of steady-state reaction systems. Canadian Journal of Chemistry 59, 737-755. doi:10.1139/v81-107
432. Chou, K. C. and Liu, W. M. (1981). Graphical rules for non-steady state enzyme kinetics. Journal of Theoretical Biology 91, 637-654. doi:10.1016/0022-5193(81)90215-0
433. Chou, K. C. (1981). A new graphical rule for rate laws of enzyme reactions with branched pathways. Canadian Journal of Biochemistry 59, 757-761. PMID:7317822
434. Chou, K. C., Chen, N. Y. and Forsen, S. (1981). The biological functions of low-frequency phonons: 2. Cooperative effects. Chemica Scripta 18, 126-132.
435. Zhou, G. P., Li, T. T. and Chou, K. C. (1981). The flexibility during the juxtaposition of reacting groups and the upper limits of enzyme reactions. Biophysical Chemistry 14, 277-281. doi:10.1016/0301-4622(81)85028-4
436. Li, T. T., Shi, Z. W., Zhou, G. Q. and Chou, K. C. (1981). A semi-analytic method for computing the concentration distribution in enzyme-substrate fast reaction systems. Journal of Computational Chemistry 2, 273-277. doi:10.1002/jcc.540020309
437. Chou, K. C. and Forsen, S. (1980). Diffusion-controlled effects in reversible enzymatic fast reaction system: Critical spherical shell and proximity rate constants. Biophysical Chemistry 12, 255-263. doi:10.1016/0301-4622(80)80002-0
438. Chou, K. C., Li, T. T. and Forsen, S. (1980). The critical spherical shell in enzymatic fast reaction systems. Biophysical Chemistry 12, 265-269. doi:10.1016/0301-4622(80)80003-2
439. Chou, K. C. and Forsen, S. (1980). Graphical rules for enzyme-catalyzed rate laws. Biochemical Journal 187, 829-835. PMID:7188428
440. Chou, K. C. (1980). A new schematic method in enzyme kinetics. European Journal of Biochemistry 113, 195-198. doi:10.1111/j.1432-1033.1980.tb06155.x
441. Chou, K. C., Forsen, S. and Zhou, G. Q. (1980). Three schematic rules for deriving apparent rate constants. Chemica Scripta 16, 109-113.
442. Chen, N. Y. and Chou, K. C. (1980). Some parametric method applied to bio-inorganic chemistry, Kexue Tongbao. (Science Bulletin in China, a semimonthly journal in English) 25, 937-941.
443. Li, T. T. and Chou, K. C. (1980). The flow of substrate molecules in fast enzyme-catalyzed reaction systems. Chemica Scripta 16, 192-196.
444. Chou, K. C., Jiang, S. P., Liu, W. M. and Fee, C. H. (1979). Graph theory of enzyme kinetics: 1. Steady-state reaction system. Scientia Sinica 22, 341-358.
445. Chou, K. C. and Chen, N. Y. (1978). Some problems in quantum biology, Huaxue Tongbao (Chemistry Bulletin in China, a monthly journal in Chinese with English abstract) 5, 29-34.
446. Chou, K. C. (1977). The kinetics of the combination reaction between enzyme and substrate: 1. Stochastic analysis, activation energy and multiple-active-site. Acta Biochimica et Biophysica Sinica 9, 79-94.
447. Chou, K. C. (1977). The kinetics of the combination reaction between enzyme and substrate: 2. Multi-barrier reaction and measuring signal. Acta Biochimica et Biophysica Sinica 9, 175-186.
448. Li, T. T. and Chou, K. C. (1977). Studies on the combination rates of liquid phase fast reaction system: Steady state process and transient phase process. Scientia Sinica 20, 197-221.
449. Chou, K. C. and Chen, N. Y. (1977). The biological functions of low-frequency phonons. Scientia Sinica 20, 447-457.
450. Li, T. T. and Chou, K. C. (1976). The quantitative relations between diffusion-controlled reaction rate and characteristic parameters in enzyme-substrate reaction system: Neutral substrate. Scientia Sinica 19, 117-136. PMID:1273571
451. Chou, K. C., Kuo, C. K. and Li, T. T. (1975). The quantitative relations between diffusion-controlled reaction rate and characteristic parameters in enzyme-substrate reaction system: Charged substrate. Scientia Sinica 18, 366-380. PMID:1198092
452. Chou, K. C. (1975). Studies on the enzyme kinetics of the cavity-active site. Acta Biochimica et Biophysica Sinica 7, 95-103.