Reviews in Computational Chemistry Volume 18

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N Scoring Functions for Receptor–Ligand Interactions 49 solvated receptor binding site O solvated receptor-ligand complex N HO O solvated ensemble of ligand conformations hydrogen bond hydrophobic contacts charge-assisted hydrogen bond Figure 3 Overview of the receptor–ligand binding process. All species involved are solvated by water (symbolized by gray spheres). The binding free energy difference between the bound and unbound state is a sum of enthalpic components (breaking and formation of hydrogen bonds, formation of specific hydrophobic contacts), and entropic components (release of water from hydrophobic surfaces to solvent, loss of conformational mobility of receptor and ligand). DESCRIPTION OF SCORING FUNCTIONS FOR RECEPTOR–LIGAND INTERACTIONS A rigorous theoretical treatment of reversible receptor–ligand binding requires full consideration of all species involved in the binding equilibrium. In the unbound state, both the ligand and the receptor are separately solvated and do not interact. In the bound state, both partners are partially desolvated and form interactions with each other. Since it is the free energy of binding one is interested in determining, the energies of the solvated receptor, the solvated ligand, and the solvated complex should be calculated as ensemble averages. O HO O
Table 1 Reference List for the Most Important Published Scoring Functions a Year Original Selected References Type of Function Name Published References to Applications 50 Empirical 1989–1993 115–117 GRID 19 SCORE1 (the LUDI 1994 56 LUDI 20,21 , e.g. 57,58 scoring function) 1994 59 FLOG 59 GOLD score 1995 60, 61 GOLD 60,61 PLP 1995, 2000 62, 63 FlexX score 1996 64 FlexX 64–67 VALIDATE 1996 68 1996 69 Hammerhead 70 ChemScore 1997 71 72 SCORE2 1998 73 1998 74 SCORE 1998 75 Fresno 1999 76 77 ScreenScore 2001 78 Desolvation terms HINT 1991 79 80 1997 81 Knowledge-based SMOG 1996 82 SMOG 83 BLEEP 1999 84, 85 PMF 1999 86 87–91 DrugScore 2000 92 93 Force field AMBER 1992 94 DOCK 94–99 CHARMM 1998 100 Force field þ desolvation 1998 101 1999 102 AMBER þ desolvation 1999 103 CHARMM þ PB 1999 104 AMBER þ desolvation 1999 105 MM PB/SA 1999 106 107, 108 Linear response simplified OWFEG 113 Grid 1994 109 110–112 free energy perturbation 2001 114 a Where force fields are used, the entry in ‘‘Original Reference’’ column refers to the use as a scoring function, not to the force field itself.
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Reviews in Computational Chemistry
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Kenny B. Lipkowitz Department of Ch
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vi Preface three-dimensional struct
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viii Preface some descriptors and i
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Epilogue and Dedication My associat
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Contents 1. Clustering Methods and
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Contents xv Electron Transfer in Po
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Contributors John M. Barnard, Barna
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Contributors to Previous Volumes *
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Volume 3 (1992) Tamar Schlick, Opti
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Volume 7 (1996) Geoffrey M. Downs a
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Volume 11 (1997) Mark A. Murcko, Re
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T. Daniel Crawford* and Henry F. Sc
Page 27 and 28: Topics Covered in Volumes 1-18 * Ab
Page 29 and 30: Reviews in Computational Chemistry
Page 31 and 32: 2 Clustering Methods and Their Uses
Page 39 and 40: 10 Clustering Methods and Their Use
Page 71 and 72: 42 The Use of Scoring Functions in
Page 77: 48 The Use of Scoring Functions in
Page 117 and 118: CHAPTER 3 Potentials and Algorithms
Page 119 and 120: Vn (1 + cos(nω + γ)) 2 K θ (θ
Page 121 and 122: are modified by their environment w
Page 123 and 124: Table 1 Polarizability Parameters f
Page 125 and 126: The polarizable point dipole models
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M i z i + q i d i k i and shell cha
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Shell Models 103 on estimates of sh
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minimization can be replaced by mor
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The energy required to create a cha
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for all i ði:e:; 8 iÞ: @U @qi l
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where we have used q Cl ¼ qNa. The
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Electronegativity Equalization Mode
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Electronegativity Equalization Mode
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of N molecules is taken as a Hartre
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is treated using variable charges.
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water have been developed, includin
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Applications 123 classical and rigi
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developing polarizable models. A va
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Comparison of the Polarization Mode
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negligible errors in such propertie
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ecome significant at field strength
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noteworthy in this regard because t
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References 135 9. P. Cieplak and P.
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References 137 48. E. L. Pollock an
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References 139 Computational Chemis
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References 141 139. J. Hinze and H.
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References 143 178. J. J. P. Stewar
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References 145 216. M. W. Mahoney a
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CHAPTER 4 New Developments in the T
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Introduction 149 applications). For
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FCWD(∆E ) FCWD(0) ∆E = 0 ∆E
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Introduction 153 Equations [6]-[12]
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Paradigm of Free Energy Surfaces 15
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Paradigm of Free Energy Surfaces 15
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In Eqs. [18] and [19], F0i is the e
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where ‘‘þ’’ and ‘‘ ’
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is, however, small for the usual co
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solute-solvent coupling through the
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where Z is the electrode overpotent
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energy surfaces of ET. 33,50-56 It
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This result indicates a fundamental
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βF i (X ) 40 20 0 −20 1 2 βλ 1
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Table 1 Main Features of the Two-Pa
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and Hss ¼ U rep ss 1 2 X j;k ðmj
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λ i /eV 4 3 2 1 0 0 10 20 30 40 Bo
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the width/Stokes shift relation (Eq
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Table 3 Mapping of the Q Model on S
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This situation is of course not sat
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F ± (Y ad )/λ I 0.8 0.4 0 −0.4
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it by choosing the GMH basis set 7
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Anharmonic higher order terms gain
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of the radiation is the perturbatio
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individual vibrational excitations
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m 12 /D 6 5.5 5 4.5 4 3.5 17 18 19
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In Eq. [144], the coordinates Y km
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ε/M −1 cm −1 4000 2000 0 analy
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βσ 2 /10 3 cm −1 14 12 10 8 Opt
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0.2 0.1 0 12 16 20 24 28 32 The app
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References 207 7. M. D. Newton, Adv
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References 209 59. R. Kubo and Y. T
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Reviews in Computational Chemistry Volume 18

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