Chemoinformatics approaches to virtual screening:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Cambridge
RSC Publ.
2008
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XVI, 338 S. Ill., graph. Darst. 25 cm |
| ISBN: | 0854041443 9780854041442 |
Internformat
MARC
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| 245 | 1 | 0 | |a Chemoinformatics approaches to virtual screening |c ed. by Alexandre Varnek ... |
| 264 | 1 | |a Cambridge |b RSC Publ. |c 2008 | |
| 300 | |a XVI, 338 S. |b Ill., graph. Darst. |c 25 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
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| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Cheminformatics | |
| 650 | 4 | |a Chemistry, Pharmaceutical |x methods | |
| 650 | 4 | |a Combinatorial Chemistry Techniques |x methods | |
| 650 | 4 | |a Computational Biology |x methods | |
| 650 | 4 | |a Computer-Aided Design | |
| 650 | 4 | |a Drug Discovery |x methods | |
| 650 | 4 | |a Drugs |x Design |x Computer simulation | |
| 650 | 4 | |a High throughput screening (Drug development) |x Computer simulation | |
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Datensatz im Suchindex
| _version_ | 1804139189493563392 |
|---|---|
| adam_text | Contents
Chapter 1 Fragment Descriptors in SAR/QSAR/QSPR Studies,
Molecular Similarity Analysis and in Virtual Screening
Igor Baskin and Alexandre Varnek
1.1 I ntroduction 1
1.2 1 iistorical Survey 2
1.3 I Vlain Characteristics of Fragment Descriptors 4
.3.1 Types of Fragments 4
.3.2 Fragments Describing Supramolecular
Systems and Chemical Reactions 14
.3.3 Storage of Fragment Information 15
.3.4 Fragment Connectivity 17
.3.5 Generic Graphs 18
.3.6 Labeling Atoms 20
1.4 / Application in Virtual Screening and In Silico Design 20
.4.1 Filtering 22
.4.2 Similarity Search 22
.4.3 SAR Classification (Probabilistic) Models 25
.4.4 QSAR/QSPR Regression Models 26
.4.5 In Silico Design 28
1.5 Limitations of Fragment Descriptors 29
1.6 Conclusion 30
Acknowledgements 30
References 30
Chapter 2 Topological Pharmacophores
Dragos Horvath
2.1 Introduction
2.1.1 3D Pharmacophore Models and Descriptors
2.1.2 Topological Pharmacophores
44
45
47
Chemoinformatics Approaches to Virtual Screening
Edited by Alexandre Varnek and Alex Tropsha
© Royal Society of Chemistry, 2008
Published by the Royal Society of Chemistry, www.rsc.org
Contents
2.2 Topological Pharmacophores from 2D-Aligments 50
2.3 Topological Pharmacophores from Pharmacophore
Fingerprints 52
2.3.1 Topological Pharmacophore Pair Fingerprints 52
2.3.2 Topological Pharmacophore Triplets 53
2.3.3 Similarity Searching with Pharmacophore
Fingerprints - Technical Issues 54
2.3.4 Similarity Searching with Pharmacophore
Fingerprints - Some Examples 58
2.3.5 Machine-learning of Topological
Pharmacophores from Fingerprints 61
2.4 Topological Index-based Pharmacophores ? 64
2.5 Conclusions 67
2.5.1 How Important is 3D Modeling for
Pharmacophore Characterization? 67
2.5.2 2D Pharmacophore Fingerprints are
Mainstream Chemoinformatics Tools, whereas
2D Pharmacophore Elucidation has been
Rarely Attempted 68
2.5.3 Each QSAR Problem should be Allowed
to Choose its Descriptors of Predilection 69
Abbreviations 72
References 72
Chapter 3 Pharmacophore-based Virtual Screening in Drug Discovery
Christian Laggner, Gerhard Wolber, Johannes Kirchmair,
Daniela Schuster and Thierry Langer
3.1 Introduction 76
3.2 Virtual Screening Methods 77
3.3 Chemical Feature-based Pharmacophores 78
3.3.1 The Term 3D Pharmacophore 79
3.3.2 Feature Definitions and Pharmacophore
Representation 79
3.4 Generation and Use of Pharmacophore Models 86
3.4.1 Ligand-based Pharmacophore Modeling 86
3.4.2 Structure-based Pharmacophore Modeling 88
3.4.3 Inclusion of Shape Information 92
3.4.4 Qualitative vs. Quantitative Pharmacophore
Models 93
3.4.5 Validation of Models for Virtual Screening 95
3.5 Application of Pharmacophore Models
in Virtual Screening 99
3.5.1 Pharmacophore Models as Part of a Multi-step
Screening Approach 101
Contents
3.5.2 Antitarget and ADME(T) Screening
Using Pharmacophores 102
3.5.3 Pharmacophore Models for Activity Profiling
and Parallel Virtual Screening 103
3.6 Pharmacophore Method Extensions and Comparisons
to Other Virtual Screening Methods 104
3.6.1 Topological Fingerprints 104
3.6.2 Shape-based Virtual Screening 106
3.6.3 Docking Methods 106
3.6.4 Pharmacophore Constraints Used in Docking 107
3.7 Further Reading 108
3.8 Summary and Conclusion 108
References 110
Chapter 4 Molecular Similarity Analysis in Virtual Screening
Lisa Peltason and Ju rgen Bajorath
4.1 Introduction 120
4.2 Ligand-based Virtual Screening 123
4.3 Foundations of Molecular Similarity Analysis 125
4.3.1 Molecular Similarity and Chemical Spaces 125
4.3.2 Similarity Measures 126
4.3.3 Activity Landscapes 127
4.3.4 Analyzing the Nature of Structure-Activity
Relationships 127
4.4 Strengths and Limitations of Similarity Methods 144
4.5 Conclusion and Future Perspectives 146
References 147
Chapter 5 Molecular Field Topology Analysis in Drug Design
and Virtual Screening
Eugene V. Radchenko, Vladimir A. Palyulin and
Nikolay S. Zefirov
5.1 Introduction: Local Molecular Parameters in QSAR,
Drug Design and Virtual Screening 150
5.2 Supergraph-based QSAR Models 153
5.2.1 Rationale and History 153
5.2.2 Molecular Field Topology Analysis (MFTA) 154
5.3 From MFTA Model to Drug Design and
Virtual Screening 162
5.3.1 MFTA Models in Biotarget and Drug Action
Analysis 162
5.3.2 MFTA Models in Virtual Screening 163
Contents
5.4 Conclusion
Acknowledgements
References
Chapter 6 Probabilistic Approaches in Activity Prediction
Dmitry Filimonov and Vladimir Poroikov
6.1 Introduction
6.2 Biological Activity
6.2.1 Dose-Effect Relationships
6.2.2 Experimental Data
6.3 Probabilistic Ligand-based Virtual Screening Methods
6.3.1 Preparation of Training Sets
6.3.2 Creation of Evaluation Sets
6.3.3 Mathematical Approaches
6.3.4 Evaluation of Prediction Accuracy
6.3.5 Single-targeted vs. Multi-targeted Virtual
Screening
6.4 PASS Approach
6.4.1 Biological Activities Predicted by PASS
Chemical Structure Description in PASS
SAR Base
Algorithm of Activity Spectrum Estimation
Interpretation of Prediction Results
Selection of the Most Prospective Compounds
6.4.2
6.4.3
6.4.4
6.4.5
6.4.6
6.5 Conclusions
References
Chapter 7 Fragment-based De Novo Design of Drug-like Molecules
Ewgenij Proschak, Yusuf Tanrikulu and Gisbert Schneider
Chapter 8
Early ADME/T Predictions: Toy or Tool?
Igor V. Tetko and Tudor I. Oprea
8.1 Introduction
8.2 Which Properties are Important for Early
Drug Discovery?
176
177
177
182
183
185
188
189
189
190
191
194
198
199
199
200
200
201
206
207
207
210
7.1 Introduction 217
7.2 From Molecules to Fragments 221
7.2.1 Pseudo-retrosynthesis 222
7.2.2 Shape-derived Fragment Definition 223
7.3 From Fragments to Molecules 225
7.4 Scoring the Design 229
7.5 Conclusions and Outlook 234
Acknowledgements 236
References 236
240
241
Contents
8.2.1 Pfizer 241
8.2.2 Abbot 242
8.2.3 Novartis 242
8.2.4 Bayer 242
8.2.5 Inpharmatica 243
8.3 Physicochemical Profiling 244
8.3.1 Lipophilicity 244
8.3.2 Solubility 246
8.4 Why Predictions Fail: The Applicability
Domain Challenge 247
8.4.1 AD Based on Similarity in the Descriptor
Space 248
8.4.2 AD Based on Similarity in the Property-based
Space 249
8.4.3 How Reliable are Physicochemical Property
Predictions? 250
8.5 Available Data for ADME/T Biological Properties 251
8.5.1 Absorption 251
8.5.2 Distribution 255
8.6 The Usefulness of ADME/T Models is Limited
by the Available Data 258
8.7 Conclusions 260
Acknowledgements 260
References 260
Chapter 9 Compound Library Design - Principles and Applications
Weifan Zheng and Stephen R. Johnson
9.1 Introduction 268
9.1.1 Compound Library Design 269
9.2 Methods for Compound Library Design 271
9.2.1 Design for Specific Biological Activities 271
9.2.2 Design for Developability or Drug-likeness 281
9.2.3 Design for Multiple Objectives and Targets
Simultaneously 285
9.3 Concluding Remarks 287
References 288
Chapter 10 Integrated Chemo- and Bioinformatics Approaches
to Virtual Screening
Alexander Tropsha
10.1 Introduction 295
10.2 Availability of Large Compound Collections
for Virtual Screening 296
10.2.1 NIH Molecular Libraries Roadmap
Initiative and the PubChem Database 297
xvi Contents
10.2.2 Other Chemical Databases in the Public
Domain 297
10.3 Structure-based Virtual Screening 297
10.3.1 Major Methodologies 298
10.3.2 Challenges and Limitations of Current
Approaches 298
10.4 Implementation of Cheminformatics Concepts
in Structure-based Virtual Screening 299
10.4.1 Predictive QSAR Models as Virtual
Screening Tools 300
10.4.2 Structure-based Chemical Descriptors
of Protein-Ligand Interface: The EnTESS
Method 306
10.4.3 Structure-based Cheminformatics Approach
to Virtual Screening: The CoLiBRI Method 311
10.5 Summary and Conclusions: Integration
of Conventional and Cheminformatics
Structure-based Virtual Screening Approaches 316
Acknowledgements 318
References 318
Subject Index 326
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| indexdate | 2024-07-09T21:40:08Z |
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| isbn | 0854041443 9780854041442 |
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| spelling | Chemoinformatics approaches to virtual screening ed. by Alexandre Varnek ... Cambridge RSC Publ. 2008 XVI, 338 S. Ill., graph. Darst. 25 cm txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Cheminformatics Chemistry, Pharmaceutical methods Combinatorial Chemistry Techniques methods Computational Biology methods Computer-Aided Design Drug Discovery methods Drugs Design Computer simulation High throughput screening (Drug development) Computer simulation Quantitative Structure-Activity Relationship QSAR (DE-588)4205429-1 gnd rswk-swf Screening (DE-588)4054045-5 gnd rswk-swf Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd rswk-swf Computational chemistry (DE-588)4290091-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Computational chemistry (DE-588)4290091-8 s Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 s QSAR (DE-588)4205429-1 s Screening (DE-588)4054045-5 s DE-604 Varnek, Alexandre Sonstige oth DE-601 pdf/application http://www.gbv.de/dms/bowker/toc/9780854041442.pdf Inhaltsverzeichnis HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017602796&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Chemoinformatics approaches to virtual screening Cheminformatics Chemistry, Pharmaceutical methods Combinatorial Chemistry Techniques methods Computational Biology methods Computer-Aided Design Drug Discovery methods Drugs Design Computer simulation High throughput screening (Drug development) Computer simulation Quantitative Structure-Activity Relationship QSAR (DE-588)4205429-1 gnd Screening (DE-588)4054045-5 gnd Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Computational chemistry (DE-588)4290091-8 gnd |
| subject_GND | (DE-588)4205429-1 (DE-588)4054045-5 (DE-588)4183784-8 (DE-588)4290091-8 (DE-588)4143413-4 |
| title | Chemoinformatics approaches to virtual screening |
| title_auth | Chemoinformatics approaches to virtual screening |
| title_exact_search | Chemoinformatics approaches to virtual screening |
| title_full | Chemoinformatics approaches to virtual screening ed. by Alexandre Varnek ... |
| title_fullStr | Chemoinformatics approaches to virtual screening ed. by Alexandre Varnek ... |
| title_full_unstemmed | Chemoinformatics approaches to virtual screening ed. by Alexandre Varnek ... |
| title_short | Chemoinformatics approaches to virtual screening |
| title_sort | chemoinformatics approaches to virtual screening |
| topic | Cheminformatics Chemistry, Pharmaceutical methods Combinatorial Chemistry Techniques methods Computational Biology methods Computer-Aided Design Drug Discovery methods Drugs Design Computer simulation High throughput screening (Drug development) Computer simulation Quantitative Structure-Activity Relationship QSAR (DE-588)4205429-1 gnd Screening (DE-588)4054045-5 gnd Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Computational chemistry (DE-588)4290091-8 gnd |
| topic_facet | Cheminformatics Chemistry, Pharmaceutical methods Combinatorial Chemistry Techniques methods Computational Biology methods Computer-Aided Design Drug Discovery methods Drugs Design Computer simulation High throughput screening (Drug development) Computer simulation Quantitative Structure-Activity Relationship QSAR Screening Struktur-Aktivitäts-Beziehung Computational chemistry Aufsatzsammlung |
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