[1]
|
Li, L., Story, M. and Legerski, R.J. (2001) Cellular re-sponses to ionizing radiation damage. Int J Radiat Oncol Biol Phys, 49, 1157-1162.
|
[2]
|
Kohn, K.W. and Pommier, Y. (2005) Molecular interac-tion map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage. Biochem Biophys Res Commun, 331, 816-827.
|
[3]
|
Perez, C.A. and Purdy, J.A. (1998) Treatment planning in radiation oncology and impact on outcome of therapy. Rays, 23, 385-426.
|
[4]
|
Tjebbes, G.W., Kreijveld, P.A., Tilanus, M.G., Hordijk, G. J. and Slootweg, P.J. (2002) P53 tumor suppressor gene mutations in laryngeal cancer and in recurrent disease following radiation therapy. Oral Oncol, 38, 296-300.
|
[5]
|
Duchting, W., Ulmer, W. and Ginsberg, T. (1996) Cancer: a challenge for control theory and computer modelling. Eur J Cancer, 32A, 1283-1292.
|
[6]
|
Ritter, M.A., Gilchrist, K.W., Voytovich, M., Chappell, R. J. and Verhoven, B.M. (2002) The role of p53 in radiation therapy outcomes for favorable-to-intermediate-risk prostate cancer. Int J Radiat Oncol Biol Phys, 53, 574-580.
|
[7]
|
Lindstrom, M.S. and Wiman, K.G. (2003) Myc and E2F1 induce p53 through p14ARF-independent mechanisms in human fibroblasts. Oncogene, 22, 4993-5005.
|
[8]
|
Pauklin, S., Kristjuhan, A., Maimets, T. and Jaks, V. (2005) ARF and ATM/ATR cooperate in p53-mediated apoptosis upon oncogenic stress. Biochem Biophys Res Commun, 334, 386-394.
|
[9]
|
Qi, J.P., Shao, S.H., Li, D.D. and Zhou, G.P. (2007) A dynamic model for the p53 stress response networks under ion radiation. Amino Acids, 33, 75-83.
|
[10]
|
Qi, J.P., Shao, S.H., Xie, J. and Zhu, Y. (2007) A mathemtical model of P53 gene regulatory networks un-der radiotherapy. Biosystems, 90, 698-706.
|
[11]
|
Ma, L., Wagner, J., Rice, J.J., Hu, W., Levine, A.J. and Stolovitzky, G.A. (2005) A plausible model for the digital response of p53 to DNA damage. Proc Natl Acad Sci USA, 102, 14266-14271.
|
[12]
|
Qi, J.P., Shao, S.H. and Shen, Y.Z. (2008) Cellular re-sponding DNA damage: An improved modeling of P53 gene regulatory networks under ion radiation (IR). Ap-plied Mathematics and Computation, 205, 73-83.
|
[13]
|
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.
|
[14]
|
Chou, K.C. (1988) Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophysical Chemistry, 30, 3-48.
|
[15]
|
Chou, K.C. (1989) Graphical rules in steady and non- steady enzyme kinetics. J. Biol. Chem., 264, 12074- 12079.
|
[16]
|
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.
|
[17]
|
Ginsberg, T., Ulmer, W. and Duchting, W. (1993) Com-puter simulation of fractionated radiotherapy: further re-sults and their relevance to percutaneous irradiation and brachytherapy. Strahlenther Onkol, 169, 304-310.
|
[18]
|
Chou, K.C., Kezdy, F.J. and Reusser, F. (1994) Review: Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Analytical Biochemistry, 221, 217-230.
|
[19]
|
Chou, K.C. (2004) Review: Structural bioinformatics and its impact to biomedical science. Current Medicinal Chemistry, 11, 2105-2134.
|
[20]
|
Chou, K.C. In Structural bioinformatics and its impact to biomedical science and drug discovery, In: Frontiers in Medicinal Chemistry. Bentham Science Publishers: The Netherlands, 3, 2006.
|
[21]
|
Huang, R.B., Du, Q.S., Wang, C.H. and 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.
|
[22]
|
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.
|
[23]
|
Wang, J.F., Gong, K., Wei, D.Q., Li, Y.X. and 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.
|
[24]
|
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 transcrip-tase inhibitor U-87201E. J. Biol. Chem., 268, 6119-6124.
|
[25]
|
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. J. Biol. Chem., 268, 14875-14880.
|
[26]
|
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.
|
[27]
|
Chou, K.C., Wei, D.Q. and Zhong, W.Z. (2003) Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. (Erratum: ibid., 2003, Vol.310, 675). Biochem Biophys Res Comm, 308, 148-151.
|
[28]
|
Du, Q.S., Wang, S.Q., Jiang, Z.Q., Gao, W.N., Li, Y.D., Wei, D.Q. and Chou, K.C. (2005) Application of bioin-formatics in search for cleavable peptides of SARS-CoV Mpro and chemical modification of octapeptides. Me-dicinal Chemistry, 1, 209-213.
|
[29]
|
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.
|
[30]
|
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.
|
[31]
|
Zheng, H., Wei, D.Q., Zhang, R., Wang, C., Wei, H. and Chou, K.C. (2007) Screening for new agonists against Alzheimer's disease. Medicinal Chemistry, 3, 488-493.
|
[32]
|
Wei, H., Wang, C.H., Du, Q.S., Meng, J. and Chou, K.C. (2009) Investigation into adamantane-based M2 inhibitors with FB-QSAR. Medicinal Chemistry, 5, 305-317.
|
[33]
|
Gong, K., Li, L., Wang, J.F., Cheng, F., Wei, D.Q. and Chou, K.C. (2009) Binding mechanism of H5N1 influ-enza virus neuraminidase with ligands and its implication for drug design. Medicinal Chemistry, 5, 242-249.
|
[34]
|
Chou, K.C. (1987) The biological functions of low- fre-quency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers, 26, 285-295.
|
[35]
|
Chou, K.C. (1989) Low-frequency resonance and coop-erativity of hemoglobin. Trends in Biochemical Sciences, 14, 212.
|
[36]
|
Schnell, J.R. and Chou, J.J. (2008) Structure and mecha-nism of the M2 proton channel of influenza A virus. Na-ture, 451, 591-595.
|
[37]
|
Gordon, G. (2008) Extrinsic electromagnetic fields, low frequency (phonon) vibrations, and control of cell func-tion: a non-linear resonance system. Journal of Biomedi- cal Science and Engineering (JBiSE), 1, 152-156 (open accessible at http://www.srpublishing.org/journal/jbise/).
|
[38]
|
Du, Q.S., Huang, R.B., Wang, C.H., Li, X.M. and 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.
|
[39]
|
Pielak, R.M., Jason, R., Schnell, J.R. and Chou, J.J. (2009) Mechanism of drug inhibition and drug resistance of in-fluenza A M2 channel. Proceedings of National Academy of Science, USA, 106, 7379-7384.
|
[40]
|
Chou, K.C. and Jiang, S.P. (1974) Studies on the rate of diffusion-controlled reactions of enzymes. Scientia Sinica, 17, 664-680.
|
[41]
|
Chou, K.C. (1984) The biological functions of low- fre-quency phonons: 3. Helical structures and microenvi-ronment. Biophysical Journal, 45, 881-890.
|
[42]
|
Chou, K.C., Kiang, Y.S. (1985) The biological functions of low-frequency phonons: 5. A phenomenological theory. Biophysical Chemistry, 22, 219-235.
|
[43]
|
Zhou, G.P. (1989) Biological functions of soliton and extra electron motion in DNA structure. Physica Scripta, 40, 698-701.
|
[44]
|
Chou, K.C., Maggiora, G.M., Mao, B. (1989) Quasi- continuum models of twist-like and accordion-like low- frequency motions in DNA. Biophysical Journal, 56, 295-305.
|
[45]
|
Chou, K.C., Zhang, C.T., Maggiora, G.M. (1994) Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth. Biopolymers, 34, 143-153.
|
[46]
|
Sinkala, Z. (2006) Soliton/exciton transport in proteins. J Theor Biol, 241, 919-927.
|
[47]
|
Chou, K.C. and Shen, H.B. (2009) FoldRate: A web- server for predicting protein folding rates from primary sequence. The Open Bioinformatics Journal, 3, 31-50 (openly acces-sible at http://www.bentham.org/open/tobioij/).
|
[48]
|
Shen, H.B., Song, J.N. and Chou, K.C. (2009) Prediction of protein folding rates from primary sequence by fusing multiple sequential features. Journal of Biomedical Sci-ence and Engineering (JBiSE), 2, 136-143 (openly ac-cessible at http://www.srpublishing.org/journal/jbise/).
|
[49]
|
Chou, K.C. and Zhang, C.T. (1992) Diagrammatization of codon usage in 339 HIV proteins and its biological im-plication AIDS. Research and Human Retroviruses, 8, 1967-1976.
|
[50]
|
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.
|
[51]
|
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.
|
[52]
|
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.
|
[53]
|
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 Theo-retical Biology, 235, 555-565.
|
[54]
|
Xiao, X., Wang, P. and 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.
|
[55]
|
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 subcellular lo-cation. Amino Acids, 30, 49-54.
|
[56]
|
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 finger-print of SARS-CoV with visualization analysis. Medicinal Chemistry, 1, 39-47.
|
[57]
|
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 Pharmaceutical and Biomedical Analysis, 41, 246-250.
|
[58]
|
Tyson, J.J. (1999) Models of cell cycle control in eu-karyotes. J Biotechnol, 71, 239-244.
|
[59]
|
Tyson, J.J. and Novak, B. (2001) Regulation of the eu-karyotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. J Theor Biol, 210, 249-263.
|
[60]
|
Magne, N., Toillon, R.A., Bottero, V., Didelot, C., Houtte, P.V., Gerard, J.P. and Peyron, J.F. (2006) NF-kappaB modulation and ionizing radiation: mechanisms and future directions for cancer treatment. Cancer Lett, 231, 158-168.
|
[61]
|
Chou, K.C., Watenpaugh, K.D. and Heinrikson, R.L. (1999) A Model of the complex between cyclin- de-pendent kinase 5 (Cdk5) and the activation domain of neuronal Cdk5 activator. Biochemical & Biophysical Re-search Communications, 259, 420-428.
|
[62]
|
Rapp, A. and Greulich, K.O. (2004) After double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available. J Cell Sci, 117, 4935-4945.
|
[63]
|
Rothkamm, K., Kruger, I., Thompson, L.H. and Lobrich, M. (2003) Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol Cell Biol, 23, 5706-5715.
|
[64]
|
Budman, J. and Chu, G. (2005) Processing of DNA for nonhomologous end-joining by cell-free extract. EMBO J, 24, 849-860.
|
[65]
|
Daboussi, F., Dumay, A., Delacote, F. and Lopez, B.S. (2002) DNA double-strand break repair signalling: the case of RAD51 post-translational regulation. Cell Signal, 14, 969-975.
|
[66]
|
Oren, M. (2003) Decision making by p53: Life, death and cancer. Cell Death Differ, 10, 431-442.
|
[67]
|
Lev Bar-Or, R., Maya, R., Segel, L.A., Alon, U., Levine, A.J. and Oren, M. (2000) Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study. Proc Natl Acad Sci U S A, 97, 11250-11255.
|
[68]
|
Weller, M. (199) Predicting response to cancer chemo-therapy: the role of p53. Cell Tissue Res, 292, 435-445.
|
[69]
|
Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A.J., Elowitz, M.B. and Alon, U. (2004) Dynam-ics of the p53-Mdm2 feedback loop in individual cells. Nat Genet, 36, 147-150.
|