Molecular modeling and simulation : an interdisciplinary guide /
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作 者：Tamar Schlick.
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ISBN：9780387954042
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简介
Summary:
Publisher Summary 1
The discovery of the DNA double helix in the 1950s prefigured the rise of molecular biology and its many offspring in the next half-century. Genomic sciences now occupy center stage and have linked the biological sciences to the chemical, physical, mathematical and computer sciences. The subject of this book, molecular modeling, represents a sub field of this successful marriage. In an accessible and easy-to-read manner the text surveys three broad topics: biomolecular structure and modeling, molecular mechanics, and simulation techniques. It provides an introduction to the field for scientists and graduate students in many disciplines, including medicine, biology, chemistry, mathematics and computer science.
Publisher Summary 2
This book evolved from an interdisciplinary graduate course entitled Molecular Modeling developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while introducing readers to the wide range of biomolecular problems being solved bycomputational techniques and to those computational tools. The book is intended for beginning graduate students in medical schools and scientific fields such as biology, chemistry, physics, mathematics, and computerscience. Other scientists who wish to enter, or become familiar, with the field of biomolecular modeling and simulation may also benefit from the broad coverage of problems and approaches.The book surveys three broad areas: biomolecular structure and modeling: current problems and state of computations; molecular mechanics: force field origin, composition, and evaluation techniques; and simulation methods: geometry optimization, Monte Carlo, and molecular dynamicsapproaches. Appendices featuring homework assignments, reading lists, and other information useful for teaching molecular modeling complement the material in the main text. Extensive use of world wide web resources is encouraged, and additional course and text information may be found on a supplementary website.Some praise for Tamar Schlick驴s 驴Molecular Modeling and Simulation: An Interdisciplinary Guide驴:||"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling.驴|驴Harold A. Scheraga, Cornell University||"A uniquely valuable introduction to the modeling of biomolecular structure and dynamics. A rigorous and up-to-date treatment of the foundations, enlivened by engaging anecdotes and historical notes.驴|驴J. Andrew McCammon, Howard Hughes Medical Institute, University of California at San Diego||"I am often asked by physicists, mathematicians and engineers to recommend a book that would be useful to get them started in computational molecular biology. I am also often approached by my colleagues in computational biology to recommend a solid textbook for a graduate course in the area. Tamar Schlick has written the book that I will be recommending to both groups. Tamar has done an amazing job in writing a book that is both suitably accessible for beginners, and suitably rigorous for experts.驴|驴J.J. Collins, Boston University
目录
Table Of Contents:
About the Cover v
Book URLs ix
Preface xi
Prelude xix
List of Figures xxxi
List of Tables xxxviii
Acronyms, Abbreviations, and Units xli
Biomolecular Structure and Modeling: Historical Perspective 1(32)
A Multidisciplinary Enterprise 2(5)
Consilience 2(1)
What is Molecular Modeling? 3(1)
Need For Critical Assessment 4(2)
Text Overview 6(1)
Molecular Mechanics 7(5)
Pioneers 7(3)
Simulation Perspective 10(2)
Experimental Progress 12(7)
Protein Crystallography 12(2)
DNA Structure 14(2)
Crystallography 16(2)
NMR Spectroscopy 18(1)
Modern Era 19(4)
Biotechnology 19(1)
PCR and Beyond 20(3)
Genome Sequencing 23(10)
Sequencing Overview 23(4)
Human Genome 27(6)
Biomolecular Structure and Modeling: Problem and Application Perspective 33(28)
Computational Challenges 33(4)
Bioinformatics 33(2)
Structure From Sequence 35(2)
Protein Folding 37(7)
Folding Views 37(2)
Folding Challenges 39(1)
Folding Simulations 40(2)
Chaperones 42(1)
Unstructured Proteins 42(2)
Protein Misfolding 44(3)
Prions 44(1)
Infectious Proteins? 44(1)
Hypotheses 45(1)
Other Misfolding Processes 46(1)
Function From Structure 47(1)
Practical Applications 47(14)
Drug Design 48(1)
AIDS Drugs 49(4)
Other Drugs 53(1)
A Long Way To Go 54(1)
Better Genes 54(2)
Designer Foods 56(3)
Designer Materials 59(1)
Cosmeceuticals 59(2)
Protein Structure Introduction 61(30)
Machinery of Life 61(5)
From Tissues to Hormones 61(1)
Size and Function Variability 62(1)
Chapter Overview 63(3)
Amino Acid Building Blocks 66(8)
Basic Cα Unit 66(1)
Essential and Nonessential Amino Acids 67(2)
Linking Amino Acids 69(3)
The Amino Acid Repertoire 72(2)
Sequence Variations in Proteins 74(6)
Globular Proteins 74(1)
Membrane and Fibrous Proteins 75(1)
Emerging Patterns from Genome Databases 76(1)
Sequence Similarity 77(3)
Protein Conformation Framework 80(11)
The Flexible φ and ψ and Rigid ω Dihedral Angles 80(4)
Rotameric Structures 84(1)
Ramachandran Plots 84(2)
Conformational Hierarchy 86(5)
Protein Structure Hierarchy 91(22)
Structure Hierarchy 92(1)
Helices 92(4)
Classic α-Helix 92(1)
310 and π Helices 93(3)
Left-Handed α-Helix 96(1)
Collagen Helix 96(1)
β-Sheets: A Common Secondary Structural Element 96(1)
Turns and Loops 96(3)
Supersecondary and Tertiary Structure 99(1)
Complex 3D Networks 99(1)
Classes in Protein Architecture 99(1)
Classes are Further Divided into Folds 100(1)
α-Class Folds 100(2)
Bundles 100(1)
Folded Leafs 101(1)
Hairpin Arrays 101(1)
β-Class Folds 102(1)
Anti-Parallel β Domains 102(1)
Parallel and Antiparallel Combinations 103(1)
α/β and α+β-Class Folds 103(2)
α/β Barrels 104(1)
Open Twisted α/β Folds 104(1)
Leucine-Rich α/β Folds 104(1)
α+β Folds 104(1)
Number of Folds 105(1)
Finite Number? 105(1)
Concerted Target Selection: Structural Genomics 105(1)
Quaternary Structure 106(5)
Viruses 106(4)
From Ribosomes to Dynamic Networks 110(1)
Structure Classification 111(2)
Nucleic Acids Structure Minitutorial 113(34)
DNA, Life's Blueprint 114(4)
The Kindled Field of Molecular Biology 114(2)
DNA Processes 116(1)
Challenges in Nucleic Acid Structure 117(1)
Chapter Overview 118(1)
Basic Building Blocks 118(8)
Nitrogenous Bases 119(1)
Hydrogen Bonds 119(1)
Nucleotides 119(2)
Polynucleotides 121(1)
Stabilizing Polynucleotide Interactions 122(2)
Chain Notation 124(1)
Atomic Labeling 125(1)
Torsion Angle Labeling 125(1)
Conformational Flexibility 126(13)
The Furanose Ring 126(5)
Backbone Torsional Flexibility 131(1)
The Glycosyl Rotation 131(1)
Sugar/Glycosyl Combinations 131(2)
Basic Helical Descriptors 133(2)
Base-Pair Parameters 135(4)
Canonical DNA Forms 139(8)
B-DNA 141(1)
A-DNA 142(3)
Z-DNA 145(1)
Comparative Features 146(1)
Topics in Nucleic Acids Structure 147(52)
Introduction 148(1)
DNA Sequence Effects 149(8)
Local Deformations 149(1)
Orientation Preferences in Dinucleotide Steps 150(3)
Intrinsic DNA Bending in A-Tracts 153(3)
Sequence Deformability Analysis Continues 156(1)
DNA Hydration and Ion Interactions 157(6)
Resolution Difficulties 159(1)
Basic Patterns 159(4)
DNA/Protein Interactions 163(2)
Variations on a Theme 165(10)
Hydrogen Bonding Patterns in Polynucleotides 165(6)
Hybrid Helical/Nonhelical Forms 171(2)
Overstretched and Understretched DNA 173(2)
RNA Structure 175(6)
RNA Chains Fold Upon Themselves 175(1)
RNA's Diversity 176(1)
RNA at Atomic Resolution 176(3)
Emerging Themes in RNA Structure and Folding 179(2)
Cellular Organization of DNA 181(5)
Compaction of Genomic DNA 181(1)
Coiling of the DNA Helix Itself 182(1)
Chromosomal Packaging of-Coiled DNA 183(3)
Mathematical Characterization of DNA Supercoiling 186(3)
DNA Topology and Geometry 186(3)
Computational Treatments of-DNA Supercoiling 189(10)
DNA as a Flexible Polymer 190(1)
Elasticity Theory Framework 191(1)
Simulations of DNA Supercoiling 192(7)
Theoretical and Computational Approaches to Biomolecular Structure 199(26)
Merging of Theory and Experiment 200(2)
Exciting Times for Computationalists! 200(2)
The Future of Biocomputations 202(1)
Chapter Overview 202(1)
QM Foundations 202(9)
The Schrodinger Wave Equation 203(1)
The Born-Oppenheimer Approximation 203(1)
Ab Initio 204(1)
Semi-Empirical QM 205(1)
Recent Advances in Quantum Mechanics 205(2)
From Quantum to Molecular Mechanics 207(4)
Molecular Mechanics Principles 211(6)
The Thermodynamic Hypothesis 211(1)
Additivity 212(2)
Transferability 214(3)
Molecular Mechanics Formulation 217(8)
Configuration Space 218(1)
Functional Form 219(3)
Some Current Limitations 222(3)
Force Fields 225(34)
Formulation of the Model and Energy 227(1)
Normal Modes 227(5)
Characteristic Motions 227(2)
Spectra of Biomolecules 229(1)
Spectra As Force Constant Sources 230(1)
In-Plane and Out-of-Plane Bending 231(1)
Bond Length Potentials 232(5)
Harmonic Term 233(1)
Morse Term 234(2)
Cubic and Quartic Terms 236(1)
Bond Angle Potentials 237(4)
Harmonic and Trigonometric Terms 237(2)
Cross Bond Stretch / Angle Bend Terms 239(2)
Torsional Potentials 241(8)
Origin of Rotational Barriers 241(1)
Fourier Terms 242(1)
Torsional Parameter Assignment 243(4)
Improper Torsion 247(1)
Cross Dihedral/Bond Angle and Improper/Improper Dihedral Terms 248(1)
van der Waals Potential 249(2)
Rapidly Decaying Potential 249(1)
Parameter Fitting From Experiment 249(1)
Two Parameter Calculation Protocols 250(1)
Coulomb Potential 251(4)
Coulomb's Law: Slowly Decaying Potential 251(2)
Dielectric Function 253(1)
Partial Charges 254(1)
Parameterization 255(4)
A Package Deal 255(1)
Force Field Performance 256(3)
Nonbonded Computations 259(46)
Computational Bottleneck 261(1)
Reducing Computational Cost 262(2)
Simple Cutoff Schemes 262(1)
Ewald and Multipole Schemes 263(1)
Spherical Cutoff Techniques 264(7)
Technique Categories 264(1)
Guidelines for Cutoff Functions 265(1)
General Cutoff Formulations 266(2)
Potential Switch 268(1)
Force Switch 269(1)
Shift Functions 270(1)
Ewald Method 271(13)
Periodic Boundary Conditions 271(3)
Ewald Sum and Crystallography 274(2)
Morphing A Conditionally Convergent Sum 276(4)
Finite-Dielectric Correction 280(1)
Ewald Sum Complexity 280(1)
Resulting Ewald Summation 281(2)
Practical Implementation 283(1)
Multipole Method 284(9)
Basic Hierarchical Strategy 285(4)
Historical Perspective 289(2)
Expansion in Spherical Coordinates 291(1)
Biomolecular Implementations 292(1)
Other Variants 293(1)
Continuum Solvation 293(12)
Need for Simplification! 293(1)
Potential of Mean Force 294(1)
Stochastic Dynamics 295(3)
Continuum Electrostatics 298(7)
Multivariate Minimization in Computational Chemistry 305(40)
Optimization Applications 306(2)
Algorithmic Understanding Needed 307(1)
Chapter Overview 307(1)
Fundamentals 308(9)
Problem Formulation 308(1)
Independent Variables 308(1)
Function Characteristics 309(1)
Local and Global Minima 310(2)
Derivatives 312(1)
Hessian Matrix 313(4)
Basic Algorithms 317(6)
Greedy Descent 317(1)
Line Searches 318(3)
Trust Region Methods 321(1)
Convergence Criteria 322(1)
Newton's Method 323(6)
Newton in One Dimension 324(3)
Newton's Method for Minimization 327(2)
Multivariate Newton 329(1)
Large-Scale methods 329(9)
Quasi-Newton (QN) 330(2)
Conjugate Gradient (CG) 332(2)
Truncated-Newton (TN) 334(2)
Simple Example 336(2)
Software 338(1)
Popular Newton and CG 338(1)
CHARMM's ABNR 338(1)
CHARMM's TN 338(1)
Comparative Performance on Molecular Systems 339(1)
Recommendations 339(3)
Future Outlook 342(3)
Monte Carlo Techniques 345(38)
Monte Carlo Popularity 346(2)
A Winning Combination 346(1)
From Needles to Bombs 347(1)
Chapter Overview 347(1)
Importance of Error Bars 348(1)
Random Number Generators 348(15)
What is Random? 348(1)
Properties of Generators? 349(3)
Linear Congruential Generators 352(4)
Other Generators 356(4)
Artifacts 360(2)
Recommendations 362(1)
Gaussian Random Variates 363(3)
Manipulation of Uniform Random Variables 363(1)
Normal Variates in Molecular Simulations 363(1)
Odeh/Evans 364(2)
Box/Muller/Marsaglia 366(1)
Monte Carlo Means 366(5)
Expected Values 366(2)
Error Bars 368(2)
Batch Means 370(1)
Monte Carlo Sampling 371(6)
Probability Density Function 371(1)
Equilibria or Dynamics 371(1)
Ensembles 372(1)
Importance Sampling 373(4)
Hybrid MC 377(6)
MC and MD 377(1)
Basic Idea 378(1)
Variants and Other Hybrid Approaches 379(4)
Molecular Dynamics: Basics 383(36)
Introduction 384(5)
Why Molecular Dynamics? 384(1)
Background 385(3)
Outline of MD Chapters 388(1)
Laplace's Vision 389(3)
The Dream 389(1)
Deterministic Mechanics 389(1)
Neglect of Electronic Motion 389(1)
Critical Frequencies 390(1)
Electron/Nuclear Treatment 391(1)
Basics 392(14)
Following Motion 392(1)
Trajectory Quality 393(1)
Initial System Settings 394(2)
Trajectory Sensitivity 396(3)
Simulation Protocol 399(1)
High-Speed Implementations 400(2)
Analysis and Visualization 402(1)
Reliable Numerical Integration 402(1)
Computational Complexity 403(3)
Verlet Algorithm 406(4)
Position and Velocity Propagation 406(2)
Leapfrog, Velocity Verlet, and Position Verlet 408(2)
Constrained Dynamics 410(2)
Various MD Ensembles 412(7)
Ensemble Types 412(1)
Simple Algorithms 413(3)
Extended System Methods 416(3)
Molecular Dynamics: Further Topics 419(44)
Introduction 420(1)
Symplectic Integrators 421(7)
Symplectic Transformation 422(1)
Harmonic Oscillator Example 422(1)
Linear Stability 423(1)
Timestep-Dependent Rotation in Phase Space 424(2)
Resonance Condition for Periodic Motion 426(1)
Resonance Artifacts 427(1)
Multiple-Timestep (MTS) Methods 428(7)
Basic Idea 428(1)
Extrapolation 429(1)
Impulses 430(1)
Resonances in Impulse Splitting 431(1)
Resonance Artifacts in MTS 431(3)
Resonance Consequences 434(1)
Langevin Dynamics 435(7)
Uses 435(1)
Heat Bath 435(1)
Effect of γ 435(2)
Generalized Verlet for Langevin Dynamics 437(1)
LN Method 438(4)
Brownian Dynamics (BD) 442(10)
Brownian Motion 442(2)
Brownian Framework 444(2)
General Propagation Framework 446(1)
Hydrodynamics 447(3)
BD Propagation 450(2)
Implicit Integration 452(7)
Implicit vs. Explicit Euler 452(2)
Intrinsic Damping 454(1)
Computational Time 454(1)
Resonance Artifacts 454(5)
Future Outlook 459(4)
Integration Ingenuity 459(1)
Current Challenges 459(4)
Similarity and Diversity in Chemical Design 463(34)
Introduction to Drug Design 464(6)
Chemical Libraries 464(1)
Early Days 465(2)
Rational Drug Design 467(2)
Automated Technology 469(1)
Chapter Overview 469(1)
Database Problems 470(5)
Database Analysis 470(1)
Similarity and Diversity Sampling 471(2)
Bioactivity 473(2)
General Problem Definitions 475(7)
The Dataset 475(1)
The Compound Descriptors 475(3)
Biological Activity 478(1)
The Target Function 479(1)
Scaling Descriptors 479(1)
The Similarity and Diversity Problems 480(2)
Data Compression and Cluster Analysis 482(10)
PCA compression 483(2)
SVD compression 485(2)
PCA and SVD 487(1)
Projection Application 488(1)
Example 489(3)
Future Perspectives 492(5)
Epilogue 497(2)
Appendix A. Molecular Modeling Sample Syllabus 499(2)
Appendix B. Article Reading List 501(4)
Appendix C. Supplementary Course Texts 505(6)
Appendix D. Homework Assignments 511(110)
Index 621
About the Cover v
Book URLs ix
Preface xi
Prelude xix
List of Figures xxxi
List of Tables xxxviii
Acronyms, Abbreviations, and Units xli
Biomolecular Structure and Modeling: Historical Perspective 1(32)
A Multidisciplinary Enterprise 2(5)
Consilience 2(1)
What is Molecular Modeling? 3(1)
Need For Critical Assessment 4(2)
Text Overview 6(1)
Molecular Mechanics 7(5)
Pioneers 7(3)
Simulation Perspective 10(2)
Experimental Progress 12(7)
Protein Crystallography 12(2)
DNA Structure 14(2)
Crystallography 16(2)
NMR Spectroscopy 18(1)
Modern Era 19(4)
Biotechnology 19(1)
PCR and Beyond 20(3)
Genome Sequencing 23(10)
Sequencing Overview 23(4)
Human Genome 27(6)
Biomolecular Structure and Modeling: Problem and Application Perspective 33(28)
Computational Challenges 33(4)
Bioinformatics 33(2)
Structure From Sequence 35(2)
Protein Folding 37(7)
Folding Views 37(2)
Folding Challenges 39(1)
Folding Simulations 40(2)
Chaperones 42(1)
Unstructured Proteins 42(2)
Protein Misfolding 44(3)
Prions 44(1)
Infectious Proteins? 44(1)
Hypotheses 45(1)
Other Misfolding Processes 46(1)
Function From Structure 47(1)
Practical Applications 47(14)
Drug Design 48(1)
AIDS Drugs 49(4)
Other Drugs 53(1)
A Long Way To Go 54(1)
Better Genes 54(2)
Designer Foods 56(3)
Designer Materials 59(1)
Cosmeceuticals 59(2)
Protein Structure Introduction 61(30)
Machinery of Life 61(5)
From Tissues to Hormones 61(1)
Size and Function Variability 62(1)
Chapter Overview 63(3)
Amino Acid Building Blocks 66(8)
Basic Cα Unit 66(1)
Essential and Nonessential Amino Acids 67(2)
Linking Amino Acids 69(3)
The Amino Acid Repertoire 72(2)
Sequence Variations in Proteins 74(6)
Globular Proteins 74(1)
Membrane and Fibrous Proteins 75(1)
Emerging Patterns from Genome Databases 76(1)
Sequence Similarity 77(3)
Protein Conformation Framework 80(11)
The Flexible φ and ψ and Rigid ω Dihedral Angles 80(4)
Rotameric Structures 84(1)
Ramachandran Plots 84(2)
Conformational Hierarchy 86(5)
Protein Structure Hierarchy 91(22)
Structure Hierarchy 92(1)
Helices 92(4)
Classic α-Helix 92(1)
310 and π Helices 93(3)
Left-Handed α-Helix 96(1)
Collagen Helix 96(1)
β-Sheets: A Common Secondary Structural Element 96(1)
Turns and Loops 96(3)
Supersecondary and Tertiary Structure 99(1)
Complex 3D Networks 99(1)
Classes in Protein Architecture 99(1)
Classes are Further Divided into Folds 100(1)
α-Class Folds 100(2)
Bundles 100(1)
Folded Leafs 101(1)
Hairpin Arrays 101(1)
β-Class Folds 102(1)
Anti-Parallel β Domains 102(1)
Parallel and Antiparallel Combinations 103(1)
α/β and α+β-Class Folds 103(2)
α/β Barrels 104(1)
Open Twisted α/β Folds 104(1)
Leucine-Rich α/β Folds 104(1)
α+β Folds 104(1)
Number of Folds 105(1)
Finite Number? 105(1)
Concerted Target Selection: Structural Genomics 105(1)
Quaternary Structure 106(5)
Viruses 106(4)
From Ribosomes to Dynamic Networks 110(1)
Structure Classification 111(2)
Nucleic Acids Structure Minitutorial 113(34)
DNA, Life's Blueprint 114(4)
The Kindled Field of Molecular Biology 114(2)
DNA Processes 116(1)
Challenges in Nucleic Acid Structure 117(1)
Chapter Overview 118(1)
Basic Building Blocks 118(8)
Nitrogenous Bases 119(1)
Hydrogen Bonds 119(1)
Nucleotides 119(2)
Polynucleotides 121(1)
Stabilizing Polynucleotide Interactions 122(2)
Chain Notation 124(1)
Atomic Labeling 125(1)
Torsion Angle Labeling 125(1)
Conformational Flexibility 126(13)
The Furanose Ring 126(5)
Backbone Torsional Flexibility 131(1)
The Glycosyl Rotation 131(1)
Sugar/Glycosyl Combinations 131(2)
Basic Helical Descriptors 133(2)
Base-Pair Parameters 135(4)
Canonical DNA Forms 139(8)
B-DNA 141(1)
A-DNA 142(3)
Z-DNA 145(1)
Comparative Features 146(1)
Topics in Nucleic Acids Structure 147(52)
Introduction 148(1)
DNA Sequence Effects 149(8)
Local Deformations 149(1)
Orientation Preferences in Dinucleotide Steps 150(3)
Intrinsic DNA Bending in A-Tracts 153(3)
Sequence Deformability Analysis Continues 156(1)
DNA Hydration and Ion Interactions 157(6)
Resolution Difficulties 159(1)
Basic Patterns 159(4)
DNA/Protein Interactions 163(2)
Variations on a Theme 165(10)
Hydrogen Bonding Patterns in Polynucleotides 165(6)
Hybrid Helical/Nonhelical Forms 171(2)
Overstretched and Understretched DNA 173(2)
RNA Structure 175(6)
RNA Chains Fold Upon Themselves 175(1)
RNA's Diversity 176(1)
RNA at Atomic Resolution 176(3)
Emerging Themes in RNA Structure and Folding 179(2)
Cellular Organization of DNA 181(5)
Compaction of Genomic DNA 181(1)
Coiling of the DNA Helix Itself 182(1)
Chromosomal Packaging of-Coiled DNA 183(3)
Mathematical Characterization of DNA Supercoiling 186(3)
DNA Topology and Geometry 186(3)
Computational Treatments of-DNA Supercoiling 189(10)
DNA as a Flexible Polymer 190(1)
Elasticity Theory Framework 191(1)
Simulations of DNA Supercoiling 192(7)
Theoretical and Computational Approaches to Biomolecular Structure 199(26)
Merging of Theory and Experiment 200(2)
Exciting Times for Computationalists! 200(2)
The Future of Biocomputations 202(1)
Chapter Overview 202(1)
QM Foundations 202(9)
The Schrodinger Wave Equation 203(1)
The Born-Oppenheimer Approximation 203(1)
Ab Initio 204(1)
Semi-Empirical QM 205(1)
Recent Advances in Quantum Mechanics 205(2)
From Quantum to Molecular Mechanics 207(4)
Molecular Mechanics Principles 211(6)
The Thermodynamic Hypothesis 211(1)
Additivity 212(2)
Transferability 214(3)
Molecular Mechanics Formulation 217(8)
Configuration Space 218(1)
Functional Form 219(3)
Some Current Limitations 222(3)
Force Fields 225(34)
Formulation of the Model and Energy 227(1)
Normal Modes 227(5)
Characteristic Motions 227(2)
Spectra of Biomolecules 229(1)
Spectra As Force Constant Sources 230(1)
In-Plane and Out-of-Plane Bending 231(1)
Bond Length Potentials 232(5)
Harmonic Term 233(1)
Morse Term 234(2)
Cubic and Quartic Terms 236(1)
Bond Angle Potentials 237(4)
Harmonic and Trigonometric Terms 237(2)
Cross Bond Stretch / Angle Bend Terms 239(2)
Torsional Potentials 241(8)
Origin of Rotational Barriers 241(1)
Fourier Terms 242(1)
Torsional Parameter Assignment 243(4)
Improper Torsion 247(1)
Cross Dihedral/Bond Angle and Improper/Improper Dihedral Terms 248(1)
van der Waals Potential 249(2)
Rapidly Decaying Potential 249(1)
Parameter Fitting From Experiment 249(1)
Two Parameter Calculation Protocols 250(1)
Coulomb Potential 251(4)
Coulomb's Law: Slowly Decaying Potential 251(2)
Dielectric Function 253(1)
Partial Charges 254(1)
Parameterization 255(4)
A Package Deal 255(1)
Force Field Performance 256(3)
Nonbonded Computations 259(46)
Computational Bottleneck 261(1)
Reducing Computational Cost 262(2)
Simple Cutoff Schemes 262(1)
Ewald and Multipole Schemes 263(1)
Spherical Cutoff Techniques 264(7)
Technique Categories 264(1)
Guidelines for Cutoff Functions 265(1)
General Cutoff Formulations 266(2)
Potential Switch 268(1)
Force Switch 269(1)
Shift Functions 270(1)
Ewald Method 271(13)
Periodic Boundary Conditions 271(3)
Ewald Sum and Crystallography 274(2)
Morphing A Conditionally Convergent Sum 276(4)
Finite-Dielectric Correction 280(1)
Ewald Sum Complexity 280(1)
Resulting Ewald Summation 281(2)
Practical Implementation 283(1)
Multipole Method 284(9)
Basic Hierarchical Strategy 285(4)
Historical Perspective 289(2)
Expansion in Spherical Coordinates 291(1)
Biomolecular Implementations 292(1)
Other Variants 293(1)
Continuum Solvation 293(12)
Need for Simplification! 293(1)
Potential of Mean Force 294(1)
Stochastic Dynamics 295(3)
Continuum Electrostatics 298(7)
Multivariate Minimization in Computational Chemistry 305(40)
Optimization Applications 306(2)
Algorithmic Understanding Needed 307(1)
Chapter Overview 307(1)
Fundamentals 308(9)
Problem Formulation 308(1)
Independent Variables 308(1)
Function Characteristics 309(1)
Local and Global Minima 310(2)
Derivatives 312(1)
Hessian Matrix 313(4)
Basic Algorithms 317(6)
Greedy Descent 317(1)
Line Searches 318(3)
Trust Region Methods 321(1)
Convergence Criteria 322(1)
Newton's Method 323(6)
Newton in One Dimension 324(3)
Newton's Method for Minimization 327(2)
Multivariate Newton 329(1)
Large-Scale methods 329(9)
Quasi-Newton (QN) 330(2)
Conjugate Gradient (CG) 332(2)
Truncated-Newton (TN) 334(2)
Simple Example 336(2)
Software 338(1)
Popular Newton and CG 338(1)
CHARMM's ABNR 338(1)
CHARMM's TN 338(1)
Comparative Performance on Molecular Systems 339(1)
Recommendations 339(3)
Future Outlook 342(3)
Monte Carlo Techniques 345(38)
Monte Carlo Popularity 346(2)
A Winning Combination 346(1)
From Needles to Bombs 347(1)
Chapter Overview 347(1)
Importance of Error Bars 348(1)
Random Number Generators 348(15)
What is Random? 348(1)
Properties of Generators? 349(3)
Linear Congruential Generators 352(4)
Other Generators 356(4)
Artifacts 360(2)
Recommendations 362(1)
Gaussian Random Variates 363(3)
Manipulation of Uniform Random Variables 363(1)
Normal Variates in Molecular Simulations 363(1)
Odeh/Evans 364(2)
Box/Muller/Marsaglia 366(1)
Monte Carlo Means 366(5)
Expected Values 366(2)
Error Bars 368(2)
Batch Means 370(1)
Monte Carlo Sampling 371(6)
Probability Density Function 371(1)
Equilibria or Dynamics 371(1)
Ensembles 372(1)
Importance Sampling 373(4)
Hybrid MC 377(6)
MC and MD 377(1)
Basic Idea 378(1)
Variants and Other Hybrid Approaches 379(4)
Molecular Dynamics: Basics 383(36)
Introduction 384(5)
Why Molecular Dynamics? 384(1)
Background 385(3)
Outline of MD Chapters 388(1)
Laplace's Vision 389(3)
The Dream 389(1)
Deterministic Mechanics 389(1)
Neglect of Electronic Motion 389(1)
Critical Frequencies 390(1)
Electron/Nuclear Treatment 391(1)
Basics 392(14)
Following Motion 392(1)
Trajectory Quality 393(1)
Initial System Settings 394(2)
Trajectory Sensitivity 396(3)
Simulation Protocol 399(1)
High-Speed Implementations 400(2)
Analysis and Visualization 402(1)
Reliable Numerical Integration 402(1)
Computational Complexity 403(3)
Verlet Algorithm 406(4)
Position and Velocity Propagation 406(2)
Leapfrog, Velocity Verlet, and Position Verlet 408(2)
Constrained Dynamics 410(2)
Various MD Ensembles 412(7)
Ensemble Types 412(1)
Simple Algorithms 413(3)
Extended System Methods 416(3)
Molecular Dynamics: Further Topics 419(44)
Introduction 420(1)
Symplectic Integrators 421(7)
Symplectic Transformation 422(1)
Harmonic Oscillator Example 422(1)
Linear Stability 423(1)
Timestep-Dependent Rotation in Phase Space 424(2)
Resonance Condition for Periodic Motion 426(1)
Resonance Artifacts 427(1)
Multiple-Timestep (MTS) Methods 428(7)
Basic Idea 428(1)
Extrapolation 429(1)
Impulses 430(1)
Resonances in Impulse Splitting 431(1)
Resonance Artifacts in MTS 431(3)
Resonance Consequences 434(1)
Langevin Dynamics 435(7)
Uses 435(1)
Heat Bath 435(1)
Effect of γ 435(2)
Generalized Verlet for Langevin Dynamics 437(1)
LN Method 438(4)
Brownian Dynamics (BD) 442(10)
Brownian Motion 442(2)
Brownian Framework 444(2)
General Propagation Framework 446(1)
Hydrodynamics 447(3)
BD Propagation 450(2)
Implicit Integration 452(7)
Implicit vs. Explicit Euler 452(2)
Intrinsic Damping 454(1)
Computational Time 454(1)
Resonance Artifacts 454(5)
Future Outlook 459(4)
Integration Ingenuity 459(1)
Current Challenges 459(4)
Similarity and Diversity in Chemical Design 463(34)
Introduction to Drug Design 464(6)
Chemical Libraries 464(1)
Early Days 465(2)
Rational Drug Design 467(2)
Automated Technology 469(1)
Chapter Overview 469(1)
Database Problems 470(5)
Database Analysis 470(1)
Similarity and Diversity Sampling 471(2)
Bioactivity 473(2)
General Problem Definitions 475(7)
The Dataset 475(1)
The Compound Descriptors 475(3)
Biological Activity 478(1)
The Target Function 479(1)
Scaling Descriptors 479(1)
The Similarity and Diversity Problems 480(2)
Data Compression and Cluster Analysis 482(10)
PCA compression 483(2)
SVD compression 485(2)
PCA and SVD 487(1)
Projection Application 488(1)
Example 489(3)
Future Perspectives 492(5)
Epilogue 497(2)
Appendix A. Molecular Modeling Sample Syllabus 499(2)
Appendix B. Article Reading List 501(4)
Appendix C. Supplementary Course Texts 505(6)
Appendix D. Homework Assignments 511(110)
Index 621
Molecular modeling and simulation : an interdisciplinary guide /
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