Chou, K. C. (2004) Review: Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11, 2105-2134.
Anfinsen, C. B. and Scheraga, H. A. (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem, 29, 205-300.
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.
Creighton, T. E. (1990) Protein folding. Biochem J, 270, 1-16.
Creighton, T. E. (1995) Protein folding. An unfolding story. Curr Biol, 5, 353-356.
Scheraga, H. A. (2008) From helix-coil transitions to protein folding. Biopolymers, 89, 479-485.
Goldberg, M. E., Semisotnov, G. V., Friguet, B., Kuwajima, K., Ptitsyn, O. B. and Sugai, S. (1990) An early immunoreactive folding intermediate of the tryptophan synthease beta 2 subunit is a 'molten globule'. FEBS Lett, 263, 51-56.
Ivankov, D. N. and Finkelstein, A. V. (2004) Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc Natl Acad Sci USA, 101, 8942-8944.
Anfinsen, C. B. (1973) Principles that govern the folding of protein chains. Science, 181, 223-230.
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.
Chou, K. C., Nemethy, G. and Scheraga, H. A. (1984) Energetic approach to packing of a-helices: 2. General treatment of nonequivalent and nonregular helices. Journal of American Chemical Society, 106, 3161-3170.
Chou, K. C., Maggiora, G. M., Nemethy, G. and Scheraga, H. A. (1988) Energetics of the structure of the four-alpha-helix bundle in proteins. Proceedings of National Academy of Sciences, USA, 85, 4295-4299.
Klein, P. and Delisi, C. (1986) Prediction of protein structural class from amino acid sequence. Biopolymers, 25, 1659-1672.
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.
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.
Chou, J. J. and Zhang, C. T. (1993) A joint prediction of the folding types of 1490 human proteins from their genetic codons. Journal of Theoretical Biology, 161, 251-262.
Chou, K. C. and Zhang, C. T. (1994) Predicting protein folding types by distance functions that make allowances for amino acid interactions. J Biol Chem, 269, 22014-22020.
Dubchak, I., Muchnik, I., Holbrook, S. R. and Kim, S. H. (1995) Prediction of protein folding class using global description of amino acid sequence. Proc Natl Acad Sci U S A, 92, 8700-8704.
Chou, K. C. (1995) Does the folding type of a protein depend on its amino acid composition? FEBS Letters, 363, 127-131.
Chou, K. C. (1995) A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Structure, Function & Genetics, 21, 319-344.
Bahar, I., Atilgan, A. R., Jernigan, R. L. and Erman, B. (1997) Understanding the recognition of protein structural classes by amino acid composition. PROTEINS: Structure, Function, and Genetics, 29, 172-185.
Zhou, G. P. (1998) An intriguing controversy over protein structural class prediction. Journal of Protein Chemistry, 17, 729- 738.
Ding, C. H. and Dubchak, I. (2001) Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics, 17, 349-358.
Zhou, G. P. and Assa-Munt, N. (2001) Some insights into protein structural class prediction. PROTEINS: Structure, Function, and Genetics, 44, 57-59.
Ding, Y. S., Zhang, T. L. and 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.
Shen, H. B. and Chou, K. C. (2006) Ensemble classifier for protein fold pattern recognition. Bioinformatics, 22, 1717-1722.
Chen, K. and Kurgan, L. (2007) PFRES: protein fold classification by using evolutionary information and predicted secondary structure. Bioinformatics, 23, 2843-2850.
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.
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.
Ouyang, Z. and Liang, J. (2008) Predicting protein folding rates from geometric contact and amino acid sequence. Protein Science, 17, 1256-1263.
Plaxco, K. W., Simons, K. T. and Baker, D. (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol, 277, 985-994.
Ivankov, D. N., Garbuzynskiy, S. O., Alm, E., Plaxco, K. W., Baker, D. and Finkelstein, A. V. (2003) Contact order revisited: influence of protein size on the folding rate. Protein Science, 12, 2057-2062.
Zhou, H. and Zhou, Y. (2002) Folding rate prediction using total contact distance. Biophys Journal, 82, 458-463.
Gromiha, M. M. and Selvaraj, S. (2001) Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J Mol Biol, 310, 27-32.
Nolting, B., Schalike, W., Hampel, P., Grundig, F., Gantert, S., Sips, N., Bandlow, W. and Qi, P. X. (2003) Structural determinants of the rate of protein folding. J Theor Biol, 223, 299-307.
Gromiha, M. M., Thangakani, A. M. and Selvaraj, S. (2006) FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res, 34, W70-74.
Wang, D., Keller, J. M., Carson, C. A., McAdo-Edwards, K. K. and Bailey, C. W. (1998) Use of fuzzy-logic-inspired features to improve bacterial recognition through classifier fusion. IEEE Trans Syst Man Cybern B Cybern, 28, 583-591.
Chou, K. C. and 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.
Chou, K. C. and Shen, H. B. (2007) Review: Recent progresses in protein subcellular location prediction. Analytical Biochemistry, 370, 1-16.
Chou, K. C. and Zhang, C. T. (1995) Review: Prediction of protein structural classes. Critical Reviews in Biochemistry and Molecular Biology, 30, 275-349.
Chou, P. Y. and Fasman, G. D. (1978) Prediction of secondary structure of proteins from amino acid sequences. Advances in Enzymology and Related Subjects in Biochemistry, 47, 45-148.
Iqbal, M. and Verrall, R. E. (1988) Implications of protein folding. Additivity schemes for volumes and compressibilities. J Biol Chem, 263, 4159-4165.
Oobatake, M. and Ooi, T. (1993) Hydration and heat stability effects on protein unfolding. Prog Biophys Mol Biol, 59, 237-284.
Jones, D. T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol, 292, 195-202.
Chou, K. C. (1999) Using pair-coupled amino acid composition to predict protein secondary structure content. Journal of Protein Chemistry, 18, 473-480.
Zhou, X. B., Chen, C., Li, Z. C. and Zou, X. Y. (2007) Using Chou's amphiphilic pseudo-amino acid composition and support vector machine for prediction of enzyme subfamily classes. Journal of Theoretical Biology, 248, 546-551.
Ding, Y. S. and Zhang, T. L. (2008) Using Chou's pseudo amino acid composition to predict subcellular localization of apoptosis proteins: an approach with immune genetic algorithm-based ensemble classifier. Pattern Recognition Letters, 29, 1887-1892.
Zhang, G. Y., Li, H. C. and Fang, B. S. (2008) Predicting lipase types by improved Chou's pseudo-amino acid composition. Protein & Peptide Letters, 15, 1132-1137.
Lin, H. (2008) The modified Mahalanobis discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. Journal of Theoretical Biology, 252, 350-356.
Li, F. M. and Li, Q. Z. (2008) Predicting protein subcellular location using Chou's pseudo amino acid composition and improved hybrid approach. Protein & Peptide Letters, 15, 612- 616.
Zhang, G. Y. and Fang, B. S. (2008) Predicting the cofactors of oxidoreductases based on amino acid composition distribution and Chou's amphiphilic pseudo amino acid composition. Journal of Theoretical Biology, 253, 310-315.
Lin, H., Ding, H., Feng-Biao Guo, F. B., Zhang, A. Y. and Huang, J. (2008) Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition. Protein & Peptide Letters, 15, 739-744.
Munteanu, C. R., Gonzalez-Diaz, H., Borges, F. and de Magalhaes, A. L. (2008) Natural/random protein classification models based on star network topological indices. Journal of Theoretical Biology, 254, 775-783.
Rezaei, M. A., Abdolmaleki, P., Karami, Z., Asadabadi, E. B., Sherafat, M. A., Abrishami-Moghaddam, H., Fadaie, M. and Forouzanfar, M. (2008) Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks. Journal of Theoretical Biology, 254, 817-820.
Chou, K. C. (1989) Graphical rules in steady and non-steady enzyme kinetics. J Biol Chem, 264, 12074-12079.
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.
Lin, S. X. and Neet, K. E. (1990) Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy. J Biol Chem, 265, 9670-9675.
Chou, K. C. and Liu, W. M. (1981) Graphical rules for non-steady state enzyme kinetics. Journal of Theoretical Biology, 91, 637-654.
Zhou, G. P. and Deng, M. H. (1984) An extension of Chou's graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochemical Journal, 222, 169-176.
Myers, D. and Palmer, G. (1985) Microcomputer tools for steady-state enzyme kinetics. Bioinformatics (original: Computer Applied Bioscience), 1, 105-110.
Kuzmic, P., Ng, K. Y. and Heath, T. D. (1992) Mixtures of tight- binding enzyme inhibitors. Kinetic analysis by a recursive rate equation. Anal Biochem, 200, 68-73.
Andraos, J. (2008) Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Canadian Journal of Chemistry, 86, 342-357.