PUBLICATIONS
Over 375 peer-review scientific papers. As of February 2010, Professor Kuo-Chen Chou's publications have been cited more than 13,200 times according to ISI Science Citation Index (Web of Science).

A. Representative Papers

  1. Chou, K.C. (2010) Graphic rule for drug metabolism systems. Current Drug Metabolism, in press.
  2. Chou, K. C. (2009). Pseudo amino acid composition and its applications in bioinformatics, proteomics and system biology. Current Proteomics, 6, 262-274.
  3. Chou, K. C. & Shen, H. B. (2009). Review: recent advances in developing web-servers for predicting protein attributes. Natural Science 2, 63-92 (openly accessible at http://www.scirp.org/journal/NS/).  
  4. Wang, J. F. and Chou, K. C. (2009). Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. Biochem  Biophys Res Comm, 390, 608-612.
  5. 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. Hum-mPLoc 2.0 web server at http://www.csbio.sjtu.edu.cn/bioinf/hum-multi-2/.
  6. 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.
  7. 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.  
  8. 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. Cell-PLoc web server at http://chou.med.harvard.edu/bioinf/Cell-PLoc/.  
  9. Chou, K. C. & Shen, H. B. (2007). Review: Recent progresses in protein subcellular location prediction. Analytical Biochemistry, 370, 1-16.  
  10. 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.
  11. 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. ProtIdent web server at  http://www.csbio.sjtu.edu.cn/bioinf/Protease/.
  12. 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; MemType-2L web server at http://chou.med.harvard.edu/bioinf/MemType/.  
  13. 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; Signal-CF web server at http://chou.med.harvard.edu/bioinf/Signal-CF/.  
  14. 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; Euk-mPLoc web server at http://chou.med.harvard.edu/bioinf/euk-multi/.  
  15. 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.
  16. Chou, K.C. (2005). Insights from modeling the 3D structure of DNA-CBF3b complex. Journal of Proteome Research, 4, 1657-1660.  
  17. Chou, K.C. (2005) Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes, Bioinformatics, 21, 10-19.  
  18. Chou, K.C. (2004) Molecular therapeutic target for type-2 diabetes, Journal of Proteome Research, 3, 1284-1288.  
  19. 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.
  20. Chou, K.C. (2004).  Review: Structural bioinformatics and its impact to biomedical science.  Current Medicinal Chemistry, 11, 2105-2134.  
  21. Chou, K.C. (2004). Modelling extracellular domains of GABA-A receptors:  subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Comm. 316, 636-642.  
  22. 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.  
  23. 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.
  24. 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.  
  25. Chou, K.C. (2001). Prediction of protein cellular attributes using pseudo-amino-acid-composition. PROTEINS: Structure, Function, and Genetics 43, 246-255.  
  26. Chou, K. C. (2000).  Review: Prediction of tight turns and their types in proteins. Analytical Biochemistry  286, 1-16.  
  27. 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.
  28. Chou, K.C. and Elrod, D.W. (1999). Protein subcellular location prediction. Protein Engineering 12, 107-118.
  29. Chou, K.C. (1996).  Review: Prediction of HIV protease cleavage sites in proteins. Analytical Biochemistry  233, 1-14.  
  30. Chou, K.C. and Zhang, C.T. (1995).  Review: Prediction of protein structural classes. Critical Reviews in Biochemistry and Molecular Biology 30, 275-349.  
  31. 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.  
  32. Chou, K.C. and 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. 
  33. Chou, K.C. (1993). A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. Journal of Biological Chemistry 268, 16938-16948.
  34. Chou, K.C. (1992). Energy-optimized structure of antifreeze protein and its binding mechanism. Journal of Molecular Biology 223, 509-517.  
  35. 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.  
  36. 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.
  37. 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.
  38. 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.  
  39. Chou, K. C. (1989). Graphical rules in steady and non-steady enzyme kinetics. Journal of Biological Chemistry 264, 12074-12079.  
  40. Chou, K. C. (1989). Low-frequency resonance and cooperativity of hemoglobin. Trends in Biochemical Sciences 14, 212.
  41. 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.  
  42. 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.  
  43. Chou, K. C. (1988). Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry 30, 3-48.  
  44. Chou, K. C. (1984). Low-frequency vibration of DNA molecules. Biochemical Journal 221, 27-31.  
  45. 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.
  46. Chou, K. C. (1984). The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophysical Journal 45, 881-890.  
  47. 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.  
  48. 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.  
  49. 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.  
  50. Chou, K. C. (1976). The kinetics of the combination reaction between enzyme and substrate. Scientia Sinica 19, 505-528.  
  51. Chou, K. C. and Jiang, S. P. (1974). Studies on the rate of diffusion-controlled reactions of enzymes. Scientia Sinica  17, 664-680.
    52.  

B. List of Others

  1. 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, in press.
  2. Xiao, X., Wang, P., Chou, K.C. (2010) Quat-2L: a web-server for predicting protein quaternary structural attributes. Molecular Diversity, DOI 10.1007/s11030-11010-19227-11038. Quat-2L web server at http://icpr.jci.jx.cn/bioinfo/Quat-2L.
  3. 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, in press, doi:10.1016/j.jtbi.2010.1001.1018. Gneg-mPLoc web server at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/.
  4. 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.
  5. 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/.
  6. 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.
  7. 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.
  8. Zhu, L., Yang, J., Song, J. N., Chou, K.C. and Shen, H. B. (2009). Improving the accuracy of predicting disulfide connectivity by feature selection. Journal of Computational Chemistry, in press. doi: 10.1002/jcc.21433
  9. 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.
  10. 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.
  11. 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.
  12. 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/.
  13. 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/.
  14. 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.
  15. 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/.
  16. 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.
  17. Shen, H.B. and Chou, K.C. (2009) Identification of proteases and their types. Analytical Biochemistry, 385, 153-160.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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/.
  35. 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/.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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/.
  51. Shen, H. B. & Chou, K.C. (2007). Signal-3L: a 3-layer approach for predicting signal peptide. Biochem  Biophys Res Comm, 363, 297-303; Signal-3L web server at http://chou.med.harvard.edu/bioinf/Signal-3L/.
  52. 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.
  53. 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/.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. Xiao, X. & Chou, K.C. (2007) Digital coding of amino acids based on hydrophobic index. Protein & Peptide Letters, 14, 871-875.
  59. 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.
  60. 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.
  61. 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/.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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/.
  69. 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.
  70. Du, Q. S., Sun, H. and Chou, K. C. (2007). Inhibitor design for SARS coronavirus main protease based on “distorted key theory”. Medicinal Chemistry, 3, 1-6.
  71. 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.
  72. 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.
  73. 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. 
  74. 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/.
  75. 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.
  76. 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.
  77. 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.
  78. Shen, H. B. and Chou, K. C. (2007). Using ensemble classifier to identify membrane protein types. Amino Acids, 32, 483-488.
  79. 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.
  80. 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.
  81. 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/.
  82. 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.
  83. 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/.
  84. 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/.
  85. 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/.
  86. Shen, H. B. and 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/.
  87. 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.
  88. 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.
  89. 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.
  90. Chou, K. C., Cai, Y.D. and Zhong, W.Z. (2006). Predicting networking couples for metabolic pathways of arabidopsis, EXCLI Journal, 5, 55-65.
  91. Chou, K. C. and Shen, H. B. (2006). Predicting protein subcellular location by fusing multiple classifiers. Journal of Cellular Biochemistry, 99, 517-527.
  92. 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.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. 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.
  98. Chou, K.C. and Cai, Y.D. (2006) Prediction of protease types in a hybridization space, Biochem.  Biophys. Res. Comm., 339, 1015-1020.
  99. 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.
  100. 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.
  101. 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.
  102. 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.
  103. 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.
  104. 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.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. 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.
  116. 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.
  117. 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.
  118. 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.
  119. Chou, K. C. (2005). Prediction of G-protein-coupled receptor classes. Journal of Proteome Research, 4, 1413-1418.
  120. Chou, K.C. (2005) Modeling the tertiary structure of human Cathepsin-E, Biochem. Biophys. Res. Commun., 331, 56-60.
  121. 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.
  122. 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.
  123. 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.
  124. 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.
  125. 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.
  126. 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.
  127. Chou, K.C. and Cai, Y.D. (2005) Predicting protein localization in budding yeast. Bioinformatics, 21, 944-950.
  128. 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.
  129. 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.
  130. 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.
  131. 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.
  132. 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.
  133. 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.
  134. 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.
  135. Cai, Y.D. and Chou, K.C. (2005) Using functional domain composition to predict enzyme family classes. Journal of Proteome Research, 4, 109-111.
  136. Du, Q., 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.
  137. 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.
  138. Chou, K.C. and Cai, Y.D. (2004) Predicting protein structural class by functional domain composition. Biochem. Biophys. Res. Comm., 321, 1007-1009.
  139. Chou, K.C. and Cai, Y.D. (2004) Using GO-PseAA predictor to predict enzyme subclass, Biochem. Biophys. Res. Comm., 325, 506-509.
  140. Cai, Y.D. and Chou, K.C. (2004) Predicting 22 protein localizations in budding yeast, Biochem. Biophys. Res. Comm., 323, 425-428.
  141. Chou, K.C. and Cai, Y.D. (2004) Predicting enzyme family class in a hybridization space, Protein Science, 13, 2857-2863.
  142. 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.
  143. 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.
  144. Chou, K.C. (2004) Insights from modeling the tertiary structure of human BACE2. Journal of Proteome Research, 3, 1069-1072.
  145. 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.
  146. 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.
  147. 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.
  148. Chou, K.C. (2004). Insights from modeling three-dimensional structures of the human potassium and sodium channels. Journal of Proteome Research, 3, 856-861.
  149. 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.
  150. 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.
  151. 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.
  152. Cai, Y.D. and Chou, K.C. (2004). Predicting subcellular localization of proteins in a hybridization space, Bioinformatics, 20, 1151-1156.
  153. 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.
  154. Yang, Z.R. and Chou, K.C. (2004). Predicting the linkage sites in glycoproteins using bio-basis function neural network, Bioinformatics, 20, 903-908.
  155. 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.
  156. Yang, Z.R. and Chou, K.C. (2004). Bio-support vector machines for computational proteomics, Bioinformatics, 20, 735-741.
  157. 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.
  158. Du, Q., Wei, D.Q., and Chou, K.C. (2003). Correlations of amino acids in proteins, Peptides, 24, 1863-1869.
  159. 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.
  160. 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.
  161. 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.
  162. 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.
  163. Cai, Y.D., Feng, K.Y., Li, Y.X., and Chou, K.C. (2003).  Support vector machine for predicting a-turn types, Peptides  24, 629-630.
  164. Chou, K.C. and Elrod, D.W. (2003). A bioinformatical analysis of enzyme family classes.  Journal of Proteome Research  2, 183-190.
  165. Cai, Y.D., Liu, X.J., Li, Y.X., Xu, X.B., and Chou, K.C. (2003). Prediction of b-turns with learning machines, Peptides  24, 665-669.
  166. 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.
  167. 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.
  168. 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. 
  169. 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.
  170. Chou, K.C. and Elrod, D.W. (2002). A bioinformatical analysis of G-protein-coupled receptors.  Journal of Proteome Research  1, 429-434.
  171. Chou, K.C. (2002). Prediction of protein signal sequences. Current Protein and Peptide Science  3, 615-622.
  172. 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.
  173. 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.
  174. 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.
  175. Cai, Y.D., Liu, X.J., Xu, X.B. and Chou, K.C. (2002). Support vector machines for the classification and prediction of b-turn types.  Journal of Peptide Science 8, 297-301.
  176. 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.
  177. 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.
  178. 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.
  179. 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.
  180. 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.
  181. 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.
  182. 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.
  183. 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.
  184. Chou, K.C. (2001). Prediction of signal peptides using scaled window.  Peptides  22, 1973-1979.
  185. Chou, K.C. (2001). Using subsite coupling to predict signal peptides. Protein Engineering  14, 75-79.
  186. 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.
  187. 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.
  188. Chou, K. C. (2000).  Prediction of protein structural classes and subcellular locations. Current Protein and Peptide Science, 1, 171-208.
  189. Chou, K. C. (2000). Prediction of protein signal sequences and their cleavage sites. PROTEINS: Structure, Function, and Genetics  42, 136-139.
  190. Chou, K. C. (2000). Prediction of protein subcellular locations by incorporating quasi-sequence-order effect. Biochem. and Biophys. Res. Commun. 278, 477-483.
  191. Cai, Y.D., Li, Y.X. and Chou, K.C. (2000). Using neural networks for prediction of domain structural classes. BBA  1476, 1-2.
  192. 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.
  193. 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.
  194. Chou, K.C. and Elrod, D.W. (1999). Prediction of membrane protein types and subcellular locations. PROTEINS: Structure, Function, and Genetics 34, 137-153.
  195. Chou, K. C. (1999). Using pair-coupled amino-acid composition to predict protein secondary structure content. Journal of Protein Chemistry  18, 473-480.
  196. 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.
  197. Cai, Y. D. and Chou, K.C. (1999).  Artificial neural network for predicting alpha-turn types. Analytical Biochemistry 268, 407-409.
  198. Liu, W. and Chou, K.C. (1999).  Protein secondary structural content prediction. Protein Engineering 12, 1041-1050.
  199. 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.
  200. Chou, K. C. (1999).  A key driving force in determination of protein structural classes. Biochem. Biophys. Res. Commun.  264, 216-224.
  201. 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.
  202. Chou, K. C. and Maggiora, G.M. (1998). Domain structural class prediction. Proteins Engineering 11, 523-538.
  203. 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.
  204. 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.
  205. Cai, Y.D., Yu, H. and Chou, K. C. (1998). Prediction of beta-turns. Journal of Protein Chemistry 17, 363-376.
  206. 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.
  207. 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.
  208. Liu, W. and Chou, K. C. (1998). Singular points of protein beta-sheets. Protein Science 7, 2324-2330.
  209. 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.
  210. Liu, W. and Chou, K. C. (1998).  Prediction of protein structural classes by modified Mahalanobis discriminant algorithm. Journal of Protein Chemistry 17, 209-217.
  211. Chou, K. C. (1997). Prediction of beta-turns in proteins. Journal of Peptide Research  49, 120-144.
  212. Chou, K. C. and Blinn, J. R. (1997). Classification and prediction of beta-turn types. Journal of Protein Chemistry  16, 575-595.
  213. 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.
  214. Chou, K. C. (1997).  Prediction and classification of alpha-turn types. Biopolymers 42, 837-853.
  215. 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.
  216. 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.
  217. 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.
  218. 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.
  219. 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.
  220. 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.
  221. Chou, K.C., Zhang, C.T.  and Elrod, D.W. (1996).  Do antisense proteins exist? Journal of Protein Chemistry  15, 59-61.
  222. 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.
  223. Cai, Y.D. and Chou, K. C. (1996). Artificial neural network model for predicting specificity of GalNAc-transferase. Analytical Biochemistry  243, 284-285.
  224. 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.
  225. 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.
  226. 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.
  227. 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.
  228. Chou, K.C. (1995) Does the folding type of a protein depend on its amino acid composition? FEBS Letters  363, 127-131.
  229. Chou, K. C. (1995) A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase. Protein Science  4, 1365-1383.
  230. Chou, K. C. (1995) The convergence-divergence duality in lectin domains of the selectin family and its implications. FEBS Letters 363 123-126.
  231. 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.
  232. 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.
  233. 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.
  234. 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.
  235. 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.
  236. 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.
  237. Zhang, C.T. and Chou, K.C. (1995). An eigenvalue-eigenvector approach to predicting protein folding types. Journal of Protein Chemistry 14, 309-326.
  238. 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.
  239. 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.
  240. Chou, K. C. (1994). A molecular piston mechanism of pumping protons by bacteriorhodopsin. Amino Acids 7, 1-17.
  241. 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.
  242. 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.
  243. 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.
  244. 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.
  245. Chou, K. C. (1993). Conformational change during photocycle of bacteriorhodopsin and its proton-pumping mechanism. Journal of Protein Chemistry 12, 337-350.
  246. 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.
  247. 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.
  248. Chou, K.C. (1993).  Prediction of protein folding types from amino acid composition by correlation angles. Amino Acids 6, 231-246.
  249. Chou, K.C. (1993). Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics. Journal of Mathematical Chemistry 12, 97-108.
  250. Chou, K.C. and Zhang, C.T. (1993). A new approach to predicting protein folding types. Journal of Protein Chemistry 12, 169-178.
  251. 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.
  252. 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.
  253. 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.
  254. 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.
  255. 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.
  256. Chou, K.C. and Zheng, C. (1992). Strong electrostatic loop-helix interactions in bundle motif protein structures. Biophysical Journal  63, 682-688.
  257. 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.
  258. 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.
  259. 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.
  260. 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.
  261. 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.
  262. 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.
  263. Chou, K.C. and Carlacci, L. (1991). Simulated annealing approach to the study of protein structures. Protein Engineering 4, 661-667.
  264. Chou, K.C. (1991). The role of loops in stabilizing bundle motif protein structures. Protein Engineering 4, 849-850.
  265. Chou, K.C. and Carlacci, L. (1991). Energetic approach to the folding of alpha/beta barrels. Proteins: Structure, Function, and Genetics 9, 280-295.
  266. 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.
  267. 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.
  268. Carlacci, L. and Chou, K.C. (1991). New development on energetic approach to the packing in proteins. Journal of Computational Chemistry 12, 410-415.
  269. Carlacci, L., Schultz, M. and Chou, K.C. (1991). Geometric and energy parameters in lysine-retinal chromophores. Protein Engineering 4, 885-889.
  270. 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.
  271. Mao, B., Maggiora, G.M. and Chou, K.C. (1991). Mass-weighted molecular dynamics simulation of cyclic polypeptides. Biopolymers 31, 1077-1086.
  272. 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.
  273. 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.
  274. Carlacci, L. and Chou, K.C. (1990). Energetic approach to the folding of four a-helices connected sequentially. Protein Engineering 3, 509-514.
  275. Carlacci, L. and Chou, K.C. (1990). Electrostatic interactions between loops and alpha-helices in 4-helix bundle proteins. Protein Engineering 4, 225-227.
  276. 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.
  277. 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.
  278. 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.
  279. Chou, K. C. and Mao, B. (1988). Collective motion in DNA and its role in drug intercalation. Biopolymers 27, 1795-1815.
  280. 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.
  281. 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.
  282. 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.
  283. 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.
  284. 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.
  285. 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.
  286. 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.
  287. Chou, K. C. and Kiang, Y. S. (1985). The biological functions of low-frequency phonons: 5. A phenomenological theory. Biophysical Chemistry 22, 219-235.
  288. Chou, K. C. (1985). Low-frequency motions in protein molecules: beta-sheet and beta-barrel. Biophysical Journal 48, 289-297.
  289. Chou, K. C. (1985). Prediction of a low-frequency mode in BPTI. International Journal of Biological Macromolecules 7, 77-80.
  290. Chou, K. C. (1984). The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition. Biophysical Chemistry 20, 61-71.
  291. 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.
  292. 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.
  293. Chou, K. C. (1983). Advances in graphical methods of enzyme kinetics. Biophysical Chemistry 17, 51-55.
  294. Chou, K. C. (1983). Low-frequency vibrations of helical structures in protein molecules. Biochemical Journal 209, 573-580.
  295. 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.
  296. Chou, K. C. (1983). Identification of low-frequency modes in protein molecules. Biochemical Journal 215, 465-469.
  297. 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.
  298. 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.
  299. 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.
  300. 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.
  301. 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.
  302. Chou, K. C. (1981). Two new schematic rules for rate laws of enzyme-catalyzed reactions. Journal of Theoretical Biology 89, 581-592.
  303. Chou, K. C. and Forsen, S. (1981). Graphical rules of steady-state reaction systems. Canadian Journal of Chemistry 59, 737-755.
  304. Chou, K. C. and Liu, W. M. (1981). Graphical rules for non-steady state enzyme kinetics. Journal of Theoretical Biology 91, 637-654.
  305. Chou, K. C. (1981). A new graphical rule for rate laws of enzyme reactions with branched pathways. Canadian Journal of Biochemistry 59, 757-761.
  306. 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.
  307. 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.
  308. 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.
  309. 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.
  310. Chou, K. C., Li, T. T. and Forsen, S. (1980). The critical spherical shell in enzymatic fast reaction systems. Biophysical Chemistry 12, 265-269.
  311. Chou, K. C. and Forsen, S. (1980). Graphical rules for enzyme-catalyzed rate laws. Biochemical Journal 187, 829-835.
  312. Chou, K. C. (1980). A new schematic method in enzyme kinetics. European Journal of Biochemistry 113, 195-198.
  313. Chou, K. C., Forsen, S. and Zhou, G. Q. (1980). Three schematic rules for deriving apparent rate constants. Chemica Scripta 16, 109-113.
  314. 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.
  315. Li, T. T. and Chou, K. C. (1980). The flow of substrate molecules in fast enzyme-catalyzed reaction systems. Chemica Scripta 16, 192-196.
  316. 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.
  317. 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.
  318. 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.
  319. 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.
  320. 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.
  321. Chou, K. C. and Chen, N. Y. (1977). The biological functions of low-frequency phonons. Scientia Sinica 20, 447-457.
  322. 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.
  323. 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.
  324. Chou, K. C. (1975). Studies on the enzyme kinetics of the cavity-active site. Acta Biochimica et Biophysica Sinica  7, 95-103.


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