Molecular modeling: basic principles and applications
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
2003
|
| Ausgabe: | 2. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | 1. Aufl. u.d.T.: Höltje, Hans-Dieter: Molecular modeling |
| Beschreibung: | XII, 228 S. Ill., graph. Darst. |
| ISBN: | 3527305890 |
Internformat
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| 245 | 1 | 0 | |a Molecular modeling |b basic principles and applications |c Hans-Dieter Höltje ... |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2003 | |
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| 650 | 7 | |a Molecular modelling |2 gtt | |
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| 650 | 4 | |a Molecules |x Models |x Computer simulation | |
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Datensatz im Suchindex
| _version_ | 1814147738341736448 |
|---|---|
| adam_text |
Titel: Molecular modeling
Autor: Höltje, Hans-Dieter
Jahr: 2003
|v
Inhalt
Preface 9
1 Introduction 1
1.1 Modern Historyof Molecular Modeling 2
1.2 Do Today's Molecular Modeling Methods Illustrate only the Lukretian
World? 3
1.3 What are Models Used for? 4
1.4 Molecular Modeling Uses All Four Types for Model Building 4
1.5 The Final Step is Design 5
1.6 The 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 10
2.1.3 Sketch Approach 12
2.1.4 Conversionof 2D Structural Data into 3D Form 12
2.2 Computational Tools for Geometry Optimization 15
2.2.1 Force Fields 35
2.2.2 Geometry Optimization 17
2.2.3 Energy-Minimizing Procedures 18
2.2.4 Use of Charges, Solvation Effects 20
2.2.5 Quantum Mechanical Methods 21
2.3 Conformational Analysis 27
2.3.1 Conformational Analysis Using Systematic Search Procedures 29
2.3.2 Conformational Analysis Using Monte Carlo Methods 32
2.3.3 Conformational Analysis Using Molecular Dynamics 33
2.4 Determination of Molecular Interaction Potentials 42
2.4.1 Molecular Electrostatic Potentials (MEPs) 42
2.4.2 Molecular Interaction Fields 50
2.4.3 Display of Properties on a Molecular Surface 56
2.5 Pharmacophore Identification 59
2.5.1 Molecules to be Matched 59
/l I Inhalt
2.5.2 Atom-by-Atom Superposition 61
2.5.3 Superposition ofMolecular Fields 63
2.6 3D QSAR Methods 65
2.6.1 The CoMFA Method 65
2.6.2 CoMFA-related Methods 69
2.6.3 More 3D QSAR Methods 70
3 A Case Study for Small Molecule Modeling:
Dopamine D3 Receptor Antagonists 173
3.1 A Pharmacophore Model for Dopamine D3 Receptor Antagonists 73
3.1.1 The Aromatk-Basic Fragment 76
3.1.2 The Spacer 78
3.1.3 The Aromatic-Amidic Residue 79
3.1.4 Resulting Pharmacophore 79
3.1.5 Molecular Interaction Fields 80
3.2 3D QSAR Analysis 82
3.2.1 Variable Reduction and PLS model 82
3.2.2 Validation of the Method 84
3.2.3 Prediction of External Ligands 85
4 Introduction to Comparative Protein Modeling 87
4.1 Where and How to get Information on Proteins 87
4.2 Terminology and Principles of Protein Structure 91
4.2.1 Conformational Properties of Proteins 91
4.2.2 Types of Secondary Structural Elements 94
4.2.3 Homologous Proteins 98
4.3 Comparative Protein Modeling 100
4.3.1 Procedures for Sequence Alignments 101
4.3.2 Determination and Generation of Structurally Conserved Regions
(SCRs) 106
4.3.3 Construction of Structurally Variable Regions (SVRs) 108
4.3.4 Side Chain Modeling 109
4.3.5 Distance Geometry Approach 111
4.3.6 Secondary Structure Prediction 111
4.3.7 Threading Methods 115
4.4 Optimization Procedures—Model Refmement—Molecular
Dynamics 119
4.4.1 Force Fields for Protein Modeling 119
4.4.2 Geometry Optimization 120
4.4.3 The Use ofMolecular Dynamics Simulations in Model Refmement 121
4.4.4 Treatment of Solvated Systems 123
4.4.5 Ligand-Binding Site Complexes 124
4.5 Validation of Protein Models 126
4.5.1 Stereochemical Accuracy 127
4.5.2 Packing Quality 131
Inhalt I VII
4.5.3 Folding Reliability 133
4.6 Properties of Proteins 138
4.6.1 Electrostatic Potential 138
4.6.2 Interaction Potentials 142
4.6.3 Hydrophobicity 142
5 Protein-based Virtual Screening 145
5.1 Preparation 145
5.1.1 Database Preparation 145
5.1.2 Representation of Proteins and Ligands 147
5.2 Docking Algorithms 149
5.2.1 Incremental Construction Methods 150
5.2.2 Genetic Algorithms 152
5.2.3 Tabu Search 253
5.2.4 Simulated Annealing and Monte Carlo Simulations 154
5.2.5 Shape-fitting Methods 155
5.2.6 Miscellaneous Approaches 155
5.3 Scoring Functions 156
5.3.1 Empirical Scoring Functions 157
5.3.2 Force Field-based Scoring Functions 158
5.3.3 Knowledge-based Scoring Functions 158
5.4 Postfiltering VS Results 159
5.4.1 Filtering by Topological Properties 159
5.4.2 Filtering by Multiple Scoring 159
5.4.3 Filtering by Combining Computational Procedures 160
5.4.4 Filtering by Chemical Diversity 161
5.4.5 Filtering by Visual Inspection 161
5.5 Comparison ofDifferent Docking and Scoring Methods 161
5.6 Examples of Successful Virtual Screening Studies 162
5.7 The Future of Virtual Screening 164
6 Scope and Limits ofMolecular Docking 169
6.1 Docking in the Polar Active Site That Contains Water Molecules -
Viral Thymidine Kinase 170
6.1.1 Setting the Scene 171
6.2 Learning from the Results 172
6.2.1 Water Contribution on dTand ACV Docking 172
6.2.2 In Search of the Binding Constant 175
6.2.3 Application to Virtual Screening 176
7 Example for the Modeling of Protein-Ligand Complexes:
Antigen Presentation by MHC Class I 179
7.1 Biochemical and Pharmacological Description of the Problem 179
7.1.1 Antigenic Proteins are Presented as Nonapeptides 180
7.1.2 Pharmacological Target: Autoimmune Reactions 180
VIII I Inhalt
7.2 Molecular Modeling of the Antigenic Complex Between a Viral Peptide
and a Class I MHC Glycoprotein 181
7.2.1 Modeling of the Ligand 181
7.2.2 Homology Modeling of the MHC Protein 183
7.3 Molecular Dynamics Studies of M H C-Peptide Complexes 192
7.3.1 HLA-A2—The Fate of the Complex during Molecular Dynamics
Simulations 192
7.3.2 HLA-B*2705 194
7.4 Analysis of Models that Emerged from Molecular Dynamics
Simulations 199
7.4.1 Hydrogen Bonding Network 200
7.4.2 Atomic Fluctuations 200
7 A3 Solvent-Accessible Surface Areas 203
7.4.4 Interaction Energies 204
7.5 SAR of the Antigenic Peptides from Molecular Dynamics
Simulations and Design of Non-natural Peptides as
High-Affinity Ligands for a MHC I Protein 206
7.5.1 The Design of New Ligands 206
7.5.2 Experimental Validation of the Designed Ligands 209
7.6 How Far Does the Model Hold? Studies on Fine Specificity
of Antigene Binding to Other MHC Proteins and Mutants 211
7.7 The T-Cell Receptor Comes in 211
7.8 Some Concluding Remarks 214
Index 217 |
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| discipline | Chemie / Pharmazie Physik Biologie Chemie |
| edition | 2. ed. |
| format | Book |
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| language | English |
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| spelling | Molecular modeling basic principles and applications Hans-Dieter Höltje ... 2. ed. Weinheim Wiley-VCH 2003 XII, 228 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier 1. Aufl. u.d.T.: Höltje, Hans-Dieter: Molecular modeling Biomolécules - Structure - Simulation par ordinateur Computersimulaties gtt Estrutura molecular (química teórica) larpcal Kristalstructuur gtt Ligands (Biochimie) - Fixation - Simulation par ordinateur Molecular modelling gtt Molécules - Modèles - Simulation par ordinateur Médicaments - Conception - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur Química farmacêutica larpcal Toepassingen gtt 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 Molekulardesign (DE-588)4265444-0 s DE-604 Höltje, Hans-Dieter Sonstige (DE-588)135841305 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010344332&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Molecular modeling basic principles and applications Biomolécules - Structure - Simulation par ordinateur Computersimulaties gtt Estrutura molecular (química teórica) larpcal Kristalstructuur gtt Ligands (Biochimie) - Fixation - Simulation par ordinateur Molecular modelling gtt Molécules - Modèles - Simulation par ordinateur Médicaments - Conception - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur Química farmacêutica larpcal Toepassingen gtt 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 |
| subject_GND | (DE-588)4265444-0 |
| 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_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 | Biomolécules - Structure - Simulation par ordinateur Computersimulaties gtt Estrutura molecular (química teórica) larpcal Kristalstructuur gtt Ligands (Biochimie) - Fixation - Simulation par ordinateur Molecular modelling gtt Molécules - Modèles - Simulation par ordinateur Médicaments - Conception - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur Química farmacêutica larpcal Toepassingen gtt 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 |
| topic_facet | Biomolécules - Structure - Simulation par ordinateur Computersimulaties Estrutura molecular (química teórica) Kristalstructuur Ligands (Biochimie) - Fixation - Simulation par ordinateur Molecular modelling Molécules - Modèles - Simulation par ordinateur Médicaments - Conception - Simulation par ordinateur Protéines - Structure - Simulation par ordinateur Química farmacêutica Toepassingen Biomolecules Structure Computer simulation Drugs Design Computer simulation Ligand binding (Biochemistry) Computer simulation Molecules Models Computer simulation Proteins Structure Computer simulation Molekulardesign |
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