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Molecular modeling: basic principles and applications

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Bibliographic Details
Format:	Book
Language:	English
Published:	Weinheim WILEY-VCH 2008
Edition:	3., rev. and exp. ed.
Subjects:	Biomolecules > Structure > Computer simulation Drugs > Design > Computer simulation Ligand binding (Biochemistry) > Computer simulation Molecules > Models > Computer simulation Proteins > Structure > Computer simulation Molekulardesign Drug Design Models, Molecular Molecular Structure Molecular Conformation Chemistry, Pharmaceutical
Online Access:	Inhaltsverzeichnis Inhaltstext Inhaltsverzeichnis
Physical Description:	X, 310 S. Ill., graph. Darst.
ISBN:	9783527315680 3527315683

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adam_txt	Contents Preface to the Third Edition X 1 Introduction 2 1.1 Modern History of Molecular Modeling 2 1.2 Do Today's Molecular Modeling Methods Only Make Pictures of the Lukretian World or Do They Make Anything More? 3 1.3 What are Models Used For? 4 1.4 Molecular Modeling Uses all Four Kinds for Model Building 5 1.5 The Final Step Is Design 5 1.6 Scope of the Book 6 2 Small Molecules 9 2.1 Generation of 3D Coordinates 9 2.1.1 Crystal Data 9 2.1.2 Fragment Libraries JO 2.1.3 Conversion of2D Structural Data into 3D Form 12 References J 5 2.2 Computational Tools for Geometry Optimization 16 2.2.1 Force Fields 16 2.2.2 Geometry Optimization 19 2.2.3 Energy-minimizing Procedures 21 2.2.4 Use of Charges, Solvation Effects 23 2.2.5 Quantum Mechanical Methods 24 References 29 2.3 Conformational Analysis 32 2.3.1 Conformational Analysis Using Systematic Search Procedures 34 2.3.2 Conformational Analysis Using Monte Carlo Methods 37 2.3.3 Conformational Analysis Using Molecular Dynamics 39 2.3.4 Which Is the Method of Choice? 44 References 46 vi Contents 2.4 Determination of Molecular Interaction Potentials 50 2.4.1 Molecular Electrostatic Potentials (MEPs) 50 2.4.2 Molecular Interaction Fields 57 2 A3 Display of Properties on a Molecular Surface 66 References 66 Further Reading 69 2.5 Pharmacophore Identification 70 2.5.1 Molecules to be Matched 70 2.5.2 Atom-by-atom Superposition 72 2.5.3 Superposition of Molecular Fields 74 References 75 2.6 3D QSAR Methods 77 2.6.1 The CoMFA Method 77 2.6.2 Other CoMFA-related Methods 81 2.6.3 More 3D QSAR Methods 83 2.6.4 Receptor-based 3D QSAR 84 2.6.5 Reliability of 3D QSAR Models 86 References 87 Further Reading 91 3 A Case Study for Small Molecule Modeling: Dopamine D3 Receptor Antagonists 93 3.1 A Pharmacophore Model for Dopamine D3 Receptor Antagonists 93 3.1.1 The Aromatic-Basic Fragment 99 3.1.2 The Spacer 100 3.1.3 The Aromatic-Amidic Residue 101 3.1.4 Resulting Pharmacophore 102 3.1.5 Molecular Interaction Fields 102 3.2 3D QSAR Analysis 104 3.2.1 Variable Reduction and PLS Model 104 3.2.2 Validation of the Model 107 3.2.3 Prediction of External Ligands 108 References 110 4 Introduction to Comparative Protein Modeling 111 4.1 Where and How to Get Information on Proteins 111 References 1 15 4.2 Terminology and Principles of Protein Structure 116 4.2.1 Conformational Properties of Proteins 116 4.2.2 Types of Secondary Structural Elements 119 4.2.3 Homologous Proteins 122 References 124 Contents I vii 4.3 Comparative Protein Modeling 126 4.3.1 Procedures for Sequence Alignments 127 4.3.2 Determination and Generation of Structurally Conserved Regions (SCRs) 133 4.3.3 Construction of Structurally Variable Regions (SVRs) 135 4.3.4 Side-Chain Modeling 136 4.3.5 Distance Geometry Approach 138 4.3.6 Secondary Structure Prediction 139 4.3.7 Threading Methods 141 References 144 4.4 Optimization Procedures - Model Refinement - Molecular Dy¬ namics 149 4.4.1 Force Fields for Protein Modeling 149 4 A.I Geometry Optimization 250 4.4.3 The Use of Molecular Dynamics Simulations in Model Refinement 151 .4,4 Treatment of Solvated Systems 153 4.4.5 Ligand-binding Site Complexes 155 References 155 4.5 Validation of Protein Models 158 4.5.1 Stereochemical Accuracy 158 4.5.2 Packing Quality 164 4.5.3 Folding Reliability 166 References 169 4.6 Properties of Proteins 173 4.6.1 Electrostatic Potential 173 4.6.2 Interaction Potentials 177 4.6.3 Hydrophobicity 177 References 1 78 5 Virtual Screening and Docking 181 5.1 Preparation of the Partners 181 5.1.1 Preparation of the Compound Librar)' 181 5.1.2 Representation of Proteins and Ligands 186 5.2 Docking Algorithms 189 5.2.1 incremental Construction Methods 189 5.2.2 Genetic Algorithms 191 5.2.3 Tabu Search 192 5.2.4 Simulated Annealing and Monte Carlo Simulations 194 5.2.5 Shape-fitting Methods 195 5.2.6 Miscellaneous Approaches 195 5.3 Scoring Functions Î96 5.3.1 Empirical Scoring Functions 196 viii I Contents 5.3.2 Force-field-based Scoring Functions 198 5.3.3 Knowledge-based Scoring Functions 198 5.3.4 Critical Overview of Fast Scoring Functions 199 5.4 Postfiltering Virtual Screening Results 200 5.4.1 Filtering by Topological Properties 200 5.4.2 Filtering by Consensus Mining Approaches 200 5.4.3 Filtering by Combining Computational Procedures 201 5.4.4 Filtering by Chemical Diversity 201 5.4.5 Filtering by Visual Inspection 202 5.5 Comparison of Different Docking and Scoring Methods 202 5.6 Examples of Successful Virtual Screening Studies 203 5.7 Outlook 206 References 207 6 Scope and Limits of Molecular Docking 217 6.1 Docking in the Polar Active Site that Contains Water Molecules 218 6.2 Including Cofactor in Docking? 225 6.3 Impact of Tautomerism on Docking 227 References 229 Further Reading 231 7 Chemogenomic Approaches to Rational Drug Design 233 7.1 Description of Ligand and Target Spaces 23 5 7.1.1 Ligand Space 236 7.1.2 Target Space 238 7.1.3 Protein-Ligand Space 240 7.2 Ligand-based Chemogenomic Approaches 242 7.2.1 Annotating Ligand Libraries 242 7.2.2 Privileged Structures 244 7.2.3 Ligand-based In alico Screening 246 7.3 Target-based Chemogenomic Approaches 249 7.3.1 Sequence-based Comparisons 249 7.3.2 Structure-based Comparisons 251 7.4 Target-Ligand-based Chemogenomic Approaches 254 7.4.1 Chemical Annotation of Target Binding Sites 254 7.4.2 Two-dimensional Searches 256 7.4.3 Three-dimensional Searches 256 7.5 Concluding Remarks 258 References 258 Contents І ix 8 A Case Study for Protein Modeling: the Nuclear Hormone Receptor CAR as an Example for Comparative Modeling and the Analysis of Protein-Ligand Complexes 265 8.1 The Biochemical and Pharmacological Description of the Problem 265 8.1.1 Nuclear Hormone Receptor Superfamily 265 8.1.2 Molecular Architecture and Activation Mechanisms of Nuclear Hormone Receptors 265 8.1.3 The Human Constitutive Active Androstan Receptor (CAR) 267 8.1.4 CARLigands 267 8.2 Comparative Modeling of the Human Nuclear Hormone Receptor CAR 268 8.2.1 Choosing Appropriate Template Structures 269 8.2.2 Homology Modeling of the Human CAR 271 8.2.3 Setting up the System for the Molecular Dynamics Simulations 271 8.3 Analysis of the Models that Emerged from MD Simulations 272 8.3.1 Atomic Fluctuations 272 8.3.2 AF-2 Interaction Domain 275 8.3.3 Deciphering the Structural Basis for Constitutive Activity of Human CAR 276 8.3.4 Coactivator Binding 278 8.4 Analysis of CAR Mutants 279 8.4.1 Identifying Important Amino Acids for CAR Activation 279 8.4.2 MD Simulations of Selected CAR Mutants 282 8.5 Modeling of CAR-Ligand Complexes 284 8.6 The CAR X-ray Structure Comes into Play 286 8.6.1 How Accurate is the Generated CAR Model? 286 8.6.2 Docking Studies Using the CAR X-ray Structure 288 8.6.3 The Basis for Constitutive Activity Revisited 289 8.7 Virtual Screening for Novel CAR Activators 292 8.8 Concluding Remarks 295 References 296 Index 299
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discipline	Chemie / Pharmazie Physik Biologie Chemie
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spelling	Molecular modeling basic principles and applications Hans-Dieter Höltje ... 3., rev. and exp. ed. Weinheim WILEY-VCH 2008 X, 310 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biomolecules Structure Computer simulation Drugs Design Computer simulation Ligand binding (Biochemistry) Computer simulation Molecules Models Computer simulation Proteins Structure Computer simulation Molekulardesign (DE-588)4265444-0 gnd rswk-swf Drug Design mesh Models, Molecular mesh Molecular Structure mesh Molecular Conformation mesh Chemistry, Pharmaceutical mesh Molekulardesign (DE-588)4265444-0 s DE-604 Höltje, Hans-Dieter Sonstige (DE-588)135841305 oth http://d-nb.info/984584978/04 Inhaltsverzeichnis text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2973440&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Regensburg https://bvbr.bib-bvb.de:443/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272591&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Molecular modeling basic principles and applications Biomolecules Structure Computer simulation Drugs Design Computer simulation Ligand binding (Biochemistry) Computer simulation Molecules Models Computer simulation Proteins Structure Computer simulation Molekulardesign (DE-588)4265444-0 gnd Drug Design mesh Models, Molecular mesh Molecular Structure mesh Molecular Conformation mesh Chemistry, Pharmaceutical mesh
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title	Molecular modeling basic principles and applications
title_auth	Molecular modeling basic principles and applications
title_exact_search	Molecular modeling basic principles and applications
title_exact_search_txtP	Molecular modeling basic principles and applications
title_full	Molecular modeling basic principles and applications Hans-Dieter Höltje ...
title_fullStr	Molecular modeling basic principles and applications Hans-Dieter Höltje ...
title_full_unstemmed	Molecular modeling basic principles and applications Hans-Dieter Höltje ...
title_short	Molecular modeling
title_sort	molecular modeling basic principles and applications
title_sub	basic principles and applications
topic	Biomolecules Structure Computer simulation Drugs Design Computer simulation Ligand binding (Biochemistry) Computer simulation Molecules Models Computer simulation Proteins Structure Computer simulation Molekulardesign (DE-588)4265444-0 gnd Drug Design mesh Models, Molecular mesh Molecular Structure mesh Molecular Conformation mesh Chemistry, Pharmaceutical mesh
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