computer modeling in molecular biology.pdf

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ContributorsV. FritschInstitut de Biologie Moleculaireet CellulaireCentre National de la RechercheScientifique15, Rue R. DescartesF-67084 StrasbourgFranceJulia M. GoodfellowDepartment of CrystallographyBirkbeck CollegeUniversity of LondonMalet StreetLondon WClE 7HXU.K.Tim J. P. HubbardCentre for Protein EngineeringMedical Research Council CentreHills RoadCambridge CB2 2QHU.K.Arthur M. LeskDepartment of HeamatologyMedical Research Council CentreHills RoadCambridge CB2 2QHU.K.David S. MossDepartment of CrystallographyBirkbeck CollegeUniversity of LondonMalet StreetLondon WClE 7HXU.K.D. J. OsguthorpeMolecular Graphics UnitSchool of ChemistryUniversity of BathBath BA2 7AYU.K.P. K. C. PaulMolecular Graphics UnitSchool of ChemistryUniversity of BathBath BA2 7AYU.K.Martine PrCvostUniversitC Libre de BruxellesUnit6 de Conformation deMacromolCculesBiologiques, CP160/16, P2Avenue P. HCgerB-1050 BruxellesBelgium
XContributorsBenoit RouxGroupe de Recherche en TransportMembranaireDtpartement de PhysiqueUniversitC de MontrCalC.P. 6128, succ. ACanada H3C 357C. Rubin-CarrezInstitut de Biologie MolCculaireet CellulaireCentre National de la RechercheScientifique15, Rue R. DescartesF-67084 StrasbourgFranceOliver S. SmartDepartment of CrystallographyBirkbeck CollegeUniversity of LondonMalet StreetLondon WClE 7HXU.K.Christopher J. ThorpeMicrobiologiskt och lhmorbiologisktCentrumKarolinska InstitutetDoetarsingen 13S-17177 StockholmSwedenDaniel Van BelleUniversitC Libre de BruxellesUnit6 de Conformation deMacromoltculesBiologiques, CP160/16, P2Avenue P. HCgerB-1050 BruxellesBelgiumE. WesthofInstitut de Biologie MolCculaireet CellulaireCentre National de la RechercheScientifique15, Rue R. DescartesF-67084 StrasbourgFranceMark A. WilliamsDepartment of CrystallographyBirkbeck CollegeUniversity of LondonMalet StreetLondon WClE 7HXU.K.Shoshana J. WodakUniversitC Libre de BruxellesUnitC de Conformation deMacromolCcules Biologiques,CP160/16, P2Avenue P. HCgerB-1050 BruxellesBelgium
Page 2 and 3: Computer Modellingin Molecular Biol
Page 5 and 6: Professor Julia M. GoodfellowDepart
Page 7: ContentsColour Illustrations ......
Page 11: Colour IllustrationsXI11Figure 4-4.
Page 14 and 15: XVIColour IllustrationsFigure 7-18.
Page 16 and 17: 2 Julia M. Goodfellow and Mark A. W
Page 22 and 23: Computer Modelling in Molecular Bio
Page 24 and 25: 2 Modellinn Protein Structures 11su
Page 26 and 27: 2 Modelling Protein Structures 13St
Page 28 and 29: 2 Modelling Protein Structures 15Th
Page 30 and 31: 2 Modelling Protein Structures 17Th
Page 32 and 33: 2 Modelling Protein Structures 19Fa
Page 34 and 35: 2 Modellinn Protein Structures 21th
Page 36 and 37: 2 Modelling Protein Structures 23ho
Page 38 and 39: 2 Modelling Protein Structures 25Wo
Page 40 and 41: 2 Modelling Protein Structures 271.
Page 42 and 43: 2.3.3 Available Modelling Programs2
Page 44 and 45: 2 Modelling Protein Structures 31sp
Page 46 and 47: 2 Modellina Protein Structures 33Ac
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Page 50 and 51: 38 D. J Osmthorue and I? K. C Paul3
Page 52 and 53: 40 D. J; Osnuthorue and I? K. C. Pa
Page 54 and 55: 42 D. J. OsPuthorDe and J? K. C Pau
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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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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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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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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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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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