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240 Oliver S. Smart[39] Halgren, T. A., Lipscomb, W. N., Chem. Phys. Lett. 1977, 49, 225-232.[40] Fischer, S., Karplus, M., Chem. Phys. Lett. 1992, 194, 252-261.[41] Liotard, D. A., Int. J; Quantum Chem. 1992, 44, 723-741.[42] Ech-Cherif El-Kettani, M. A., Durup, J., Biopolymers 1992, 32, 561 -574.[43] Schlitter, J., Engels, M., Kruger, P., Jacoby, E., Wollmer, A., Mol. Simul. 1993, 10,291 -308.[44] Czerminski, R., Elber, R., Znt. J; Quantum Chem. 1990, S24, 167-186.[45] Nowak, W., Czerminski, R., Elber, R., J; Am. Chem. SOC. 1991, 113, 5627-5637.[46] Fletcher, R., Reeves, C. M., Comput. J; 1964, 7, 149-154.[47] Polak, E., Computational Methods in Optimization, Academic Press, New York 1971.[48] Press, W. H., Flannery, B. P., Teukolsky, S. A., Vetterling, W. T., Numerical Recipes, TheArt of Scientific Computing, Cambridge University Press, Cambridge, 1986.[49] Kirkpatrick, S., Gelatt, C. D. Jr., Vecchi, M. P., Science 1983, 220, 671-680.[50] Elber, R., Karplus, M., Chem. Phys. Lett. 1987, 139, 375-380.[Sl] Czerminski, R., Roitberg, A., Choi, C., Utilsky, A., Elber, R., in: AZP Conference Proceedings239 - Advances in Biomolecular Simulations, Lavery, R., Rivail, J.-L., Smith,J. (eds.), American Institute of Physics, New York 1991, pp. 153-173.[521 Smart, 0. S., Chem. Phys. Letts. 1994, 222, 503-512.[53] Cremer, D., Pople, J. A., J; Am. Chem. SOC. 1975, 97, 1354-1358.[54] Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta,S. Jr., Weiner, P., J; Am. Chem. SOC. 1984, 106, 765-784.[55] Chen, W.-P., Proc. Biochem. 1980, 15, 36-41.[56] Collyer, C. A., Henrick, K., Blow, D. M., J; Mol. Biol. 1990, 212, 211-235.1571 Whitlow, M., Howard, A. J., Finzel, B. C., Poulos, T. L., Winbourne, E., Gilliland, G.L., Proteins 1991, 9, 153-173.[58] Dietz, W., Riede, W. O., Heinzinger, K., 2. Naturforsch. 1982, 37a, 1038-1048.1591 Danno, G., Agr. Biol. Chem., 1970, 34, 1805-1814.[60] Aqvist, J., J; Phys. Chem. 1990, 94, 8021-8024.[61] Wako, H., G6, N. J; Comp. Chem. 1987, 8, 625-635.
Computer Modelling in Molecular BiologyEdited by Julia M. GoodfellowOVCH Verlagsgesellschaft mbH, 1995IndexAAccessible surface area 73Accessible volume 73Accuracy of modelling 32Activated dynamics 155Active conformation 38Adiabatic mapping method 218Agonists 38AMBER 14, 108, 227Antagonists 38Antibody response 172Anticodon hairpin 123 - 125Antigen 172Antigen binding loops 25-27Association constants 62Atomic fluctuations 120- 121Autocorrelation function 120- 121BB-factors 104Barnase 61ppBrugel 70CCellular immune system 172Channel conductance 138, 160Channel, internal waters 147- 148CHARMM 15, 65, 143COMPOSER 191Computer simulation 2Conformational search 46Conformational transitions 44, 215 ppContra MD method 219Coulombic interaction 66Counterions 116Cut-off distance 67DDatabase screening 24, 25De novo design 52Dielectric constant 108, 109Diffusion coefficients 84-85Diffusion of water 146Distance geometry 43DNA- molecular dynamics 118- phosphate screening 106- polymorphism 106EEnergy calculations 24, 28- methods 42Energy minization 2, 28, 38, 46, 218,225Energy profile 227, 235Ensembles 113Enzyme ligand complexes 61Epstein Barr virus nucelar antigenpeptide 198ppEquilibration 110Error estimation 94FFlexibility 5, 38, 51Force field 65Free energy 43, 61 pp, 86pp- coupling parameter 43- difference 87- pathways 89, 92- perturbation method 86, 88- practical aspects 88- profile 138- thermodynamic integration 43, 87
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Computer Modellingin Molecular Biol
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Professor Julia M. GoodfellowDepart
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ContentsColour Illustrations ......
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XContributorsBenoit RouxGroupe de R
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Colour IllustrationsXI11Figure 4-4.
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XVIColour IllustrationsFigure 7-18.
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2 Julia M. Goodfellow and Mark A. W
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Computer Modelling in Molecular Bio
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2 Modellinn Protein Structures 11su
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2 Modelling Protein Structures 13St
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2 Modelling Protein Structures 15Th
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2 Modelling Protein Structures 17Th
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2 Modelling Protein Structures 19Fa
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2 Modellinn Protein Structures 21th
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2 Modelling Protein Structures 23ho
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2 Modelling Protein Structures 25Wo
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2 Modelling Protein Structures 271.
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2.3.3 Available Modelling Programs2
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2 Modelling Protein Structures 31sp
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2 Modellina Protein Structures 33Ac
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2 Modelling Protein Structures 35[8
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38 D. J Osmthorue and I? K. C Paul3
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40 D. J; Osnuthorue and I? K. C. Pa
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42 D. J. OsPuthorDe and J? K. C Pau
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~443.3.1D. J. Osnuthorpe and I? K.
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46 D. 1 Osnuthorpe and r! K. C. Pau
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48 D. J. Osguthorpe and I? K. C. Pa
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50 D. J. Osguthorpe and I? K. C. Pa
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52 D. J. Osguthorpe and I! K. C. Pa
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4 Molecular Dynamics and Free Energ
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4 Molecular Dvnamics and Free Enera
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4 Molecular Dynamics and Free Enerw
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4 Molecular Dynamics and Free Enern
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5 Modelling Nucleic Acids 105and it
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5 Modelling Nucleic Acids 107of the
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5 Modelling Nucleic Acids 109ElFigu
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5 Modelling Nucleic Acids 11 1Figur
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5 Modellinn Nucleic Acids 1135.7 Ch
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5 Modelling Nucleic Acids 115With i
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5 Modellinn Nucleic Acids 117Figure
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5 Modelling Nucleic Acids 119Figure
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5 Modelling Nucleic Acids 1211.0mod
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5 Modelling Nucleic Acids 1235.12 M
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5 Modelling Nucleic Acids 125rotati
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5 Modellinp Nucleic Acids 1275.14 M
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5 Modelling Nucleic Acids 129simula
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5 Modellinn Nucleic Acids 131[40] G
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134 Benoft Roux6.1 IntroductionThe
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136 Benoit Roux[18-201. The gramici
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138 Benoft Rouxwhere D (x) is the l
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140 Benoft Roux“one-ion” conduc
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142 Benoft RouxTable 6-1. Interacti
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144 Benoit RouxFigure 6-2. Solvated
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146 Benoit Rouxwater box equilibrat
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148 Benoit Roux-I I I I II I I I II
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150 Benoi’t Rouxbulk waters. A st
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152 Benoit RouxOne advantage of thi
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154 Benoft Roux-.3.-15-c 10 -h5 5 -
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156 Benoft Rouxwhere x and v are th
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158 Benoit RouxReactant to ProductO
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160 Benoit Rouxremain in close cont
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162 Benoit Rouxis the deviation of
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164 Benoft RouxTable 6-3. Pre-expon
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166 Benoft RouxThis chapter demonst
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168 Benoft Rouxproximately one Kf c
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7 Major Histocompatibility Complex
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7 Major HistocompatibiIity Complex
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7 Maior Histocompatibility Complex
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7 Maior Histocomuatibilitv Cornulex
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Page 224 and 225: 216 Oliver S. Smart8.1 Introduction
Page 226 and 227: 218 Oliver S. Smartvolving large mo
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Page 234 and 235: 226 Oliver S. Smart8.4 Applications
Page 236 and 237: 228 Oliver S. Smartrigid-body penal
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Page 240 and 241: 232 Oliver S. SmartrbFigure 8-5. A
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Page 244 and 245: 236 Oliver S. Smarttermediates mark
Page 246 and 247: 238 Oliver S. Smartmoving conformat
Page 250 and 251: 242 IndexGGramicidin A 134- NMR dat
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