Molecular modeling: basic principles and applications
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Weinheim
WILEY-VCH
2008
|
| Ausgabe: | 3., rev. and exp. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | X, 310 S. Ill., graph. Darst. |
| ISBN: | 9783527315680 3527315683 |
Internformat
MARC
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| 020 | |a 3527315683 |c Pb. : ca. EUR 55.00 (freier Pr.), ca. sfr 88.00 (freier Pr.) |9 3-527-31568-3 | ||
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| 245 | 1 | 0 | |a Molecular modeling |b basic principles and applications |c Hans-Dieter Höltje ... |
| 250 | |a 3., rev. and exp. ed. | ||
| 264 | 1 | |a Weinheim |b WILEY-VCH |c 2008 | |
| 300 | |a X, 310 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Biomolecules |x Structure |x Computer simulation | |
| 650 | 4 | |a Drugs |x Design |x Computer simulation | |
| 650 | 4 | |a Ligand binding (Biochemistry) |x Computer simulation | |
| 650 | 4 | |a Molecules |x Models |x Computer simulation | |
| 650 | 4 | |a Proteins |x Structure |x Computer simulation | |
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| 700 | 1 | |a Höltje, Hans-Dieter |e Sonstige |0 (DE-588)135841305 |4 oth | |
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| 856 | 4 | 2 | |q text/html |u http://deposit.dnb.de/cgi-bin/dokserv?id=2973440&prov=M&dok_var=1&dok_ext=htm |3 Inhaltstext |
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Datensatz im Suchindex
| _version_ | 1805089794164785152 |
|---|---|
| adam_text |
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 |
| 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 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author_GND | (DE-588)135841305 |
| building | Verbundindex |
| bvnumber | BV023069430 |
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| callnumber-label | QP517 |
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| callnumber-search | QP517.M3 |
| callnumber-sort | QP 3517 M3 |
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| classification_tum | CHE 615f CHE 130f CHE 806f CHE 026f |
| ctrlnum | (OCoLC)191889943 (DE-599)DNB984584978 |
| dewey-full | 572.330113 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
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| dewey-search | 572.330113 |
| dewey-sort | 3572.330113 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Physik Biologie Chemie |
| discipline_str_mv | Chemie / Pharmazie Physik Biologie Chemie |
| edition | 3., rev. and exp. ed. |
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| id | DE-604.BV023069430 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:32:23Z |
| indexdate | 2024-07-20T09:29:35Z |
| institution | BVB |
| isbn | 9783527315680 3527315683 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016272591 |
| oclc_num | 191889943 |
| open_access_boolean | |
| owner | DE-91G DE-BY-TUM DE-703 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-29T DE-526 DE-634 DE-M49 DE-BY-TUM DE-11 DE-188 DE-578 DE-83 DE-B768 |
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| physical | X, 310 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | WILEY-VCH |
| record_format | marc |
| 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 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 application/pdf http://bvbr.bib-bvb.de:8991/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 |
| 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_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 |
| topic_facet | Biomolecules Structure Computer simulation Drugs Design Computer simulation Ligand binding (Biochemistry) Computer simulation Molecules Models Computer simulation Proteins Structure Computer simulation Molekulardesign |
| url | http://d-nb.info/984584978/04 http://deposit.dnb.de/cgi-bin/dokserv?id=2973440&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016272591&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT holtjehansdieter molecularmodelingbasicprinciplesandapplications |
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