computer modeling in molecular biology.pdf

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162 Benoit Rouxis the deviation of the instantaneous force relative to the average force acting on theion constrained at the barrier top [39, 91, 921. The integrand in Eq. (6-33), i.e.,
6 Theory of Thansport in Ion Channels 163c.-10c..g 0.84c8 0.6c9)n4 0.4Ei= 0.2- w'0.-g obz-0.2d\ I1 I ,0 0.1 0.2 0.3 0.4t inpsFigure 6-8. Decomposition of the normalized time-dependent friction of Na+ ion,t(t)/[(O), calculated at the transition state (solid line). The water-water contributiont,, (t)/((O) (dashed line), the channel-channel (cc(t)/((0)(short-dashed line), and the waterchannelcross terms [(,(t) + (wc(t)]/((0) (dotted line) are also shown. The rootisequal to 483 kJ/mol/nm. The total friction calculated frommean-square force, v m,Eq. (6-33) corresponds to a diffusion constant of 0.64 x lop5 cm2/s, i. e., less than one thirdof the experimental diffusion constant of Na+ in bulk water [l]; with (, TCc and [(,(t) +
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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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54 D. L Osguthorpe and I! K. C Paul
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56 D. J Osguthorpe and I? K. C. Pau
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58 D. J. Osguthorpe and r! 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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Page 144 and 145: 134 Benoft Roux6.1 IntroductionThe
Page 146 and 147: 136 Benoit Roux[18-201. The gramici
Page 148 and 149: 138 Benoft Rouxwhere D (x) is the l
Page 150 and 151: 140 Benoft Roux“one-ion” conduc
Page 152 and 153: 142 Benoft RouxTable 6-1. Interacti
Page 154 and 155: 144 Benoit RouxFigure 6-2. Solvated
Page 156 and 157: 146 Benoit Rouxwater box equilibrat
Page 158 and 159: 148 Benoit Roux-I I I I II I I I II
Page 160 and 161: 150 Benoi’t Rouxbulk waters. A st
Page 162 and 163: 152 Benoit RouxOne advantage of thi
Page 164 and 165: 154 Benoft Roux-.3.-15-c 10 -h5 5 -
Page 166 and 167: 156 Benoft Rouxwhere x and v are th
Page 168 and 169: 158 Benoit RouxReactant to ProductO
Page 170 and 171: 160 Benoit Rouxremain in close cont
Page 174 and 175: 164 Benoft RouxTable 6-3. Pre-expon
Page 176 and 177: 166 Benoft RouxThis chapter demonst
Page 178 and 179: 168 Benoft Rouxproximately one Kf c
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7 Major Histocompatibility Complex
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216 Oliver S. Smart8.1 Introduction
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218 Oliver S. Smartvolving large mo
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220 Oliver S. Smart8.2 TheoryConsid
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222 Oliver S. Smart(8-2)and applyin
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224 Oliver S. SmartThe repulsion te
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226 Oliver S. Smart8.4 Applications
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228 Oliver S. Smartrigid-body penal
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230 Oliver S. Smart216 252 200 324
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232 Oliver S. SmartrbFigure 8-5. A
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234 Oliver S. Smartlink the eoc and
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236 Oliver S. Smarttermediates mark
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238 Oliver S. Smartmoving conformat
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240 Oliver S. Smart[39] Halgren, T.
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242 IndexGGramicidin A 134- NMR dat
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