computer modeling in molecular biology.pdf

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PrefaceComputer simulation studies have advanced along way from the studies onmonatomic fluids such as argon and molecular liquids such as water. Even the earlypioneering explorations of macromolecular conformation, which were only achievedwith the greatest technical expertise, look simple in comparison to what can beachieved in the 1990s. These advances have occurred because of the increasing speedof computer hardware whether scalar, vector or parallel as well as the availability ofsoftware.This book provides a series of snap-shots of the use of molecular simulationtechniques to study a wide-range of biological problems. I hope you will not onlysee the current successes but also realize that there is still much further to go. Weare still limited to the picosecond and nanosecond time range and to relatively smallmacromolecules when the biology demands that we study the behaviour ofmacromolecular assemblies on millisecond timescales. There are many other grandchallenges ahead including the better incorporation of quantum mechanical effects,within large molecular systems, and the use of more realistic electrostatic models forboth short and long range calculations. It will be of interest to see how molecularmodelling develops over the next few years and whether it continues to progress asfast as the previous ten years and if it can keep pace with the exponential increasein experimental data on both sequences and structure of biological macromolecules.London, May 1995Julia M. Goodfellow
ContentsColour Illustrations ..........................................XI -XVIIntroduction to Computer Simulation: Methods and Applications.. ....Julia M. Goodfellow and Mark A. Williams1Modelling Protein Structures ...................................... 9Tim J. I! Hubbard and Arthur M. LeskMolecular Dynamics Simulations of Peptides ........................D. J. Osgufhorpe and I? K. C PaulMolecular Dynamics and Free Energy Calculations Applied to theEnzyme Barnase and One of its Stability Mutants.. ..................Shoshana J. Wodak, Daniel van Belle, and Martine Prkvost3761The Use of Molecular Dynamics Simulations for ModellingNucleic Acids .................................................... 103E. WesthoJ C. Rubin-Carrez, and K FritschTheory of Transport in Ion Channels.. .............................Benoit RouxMolecular Modelling and Simulations of Major HistocompatibilityComplex Class I Protein-Peptide Interactions ........................Christopher .J# Thorpe and David S. MossPath Energy Minimization: A New Method for the Simulation ofConformational Transitions of Large Molecules ......................Oliver S. Smart13317 1215Index ........................................................... 241
Page 2 and 3: Computer Modellingin Molecular Biol
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Computer Modelling in Molecular Bio
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4 Molecular Dynamics and Free Energ
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4 Molecular Dvnamics and Free Enera
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5 Modelling Nucleic Acids 105and it
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5 Modellinp Nucleic Acids 1275.14 M
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5 Modelling Nucleic Acids 129simula
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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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HLA-B*270 IHLA-B*2702HLA-B*2703HLA-
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7 Maior Histocomvatibilitv Comrdex
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216 Oliver S. Smart8.1 Introduction
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218 Oliver S. Smartvolving large mo
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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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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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