|  | Sotriffer, Christoph (ed.)
Virtual Screening
Principles, Challenges, and Practical Guidelines
Methods and Principles in Medicinal Chemistry (Volume 48)
Edited by Mannhold, Raimund / Kubinyi, Hugo / Folkers, Gerd
 1. Edition January 2011
149.- Euro
2011. XXX, 520 Pages, Hardcover
101 Fig. (49 Colored Fig.), 26 Tab.
- Handbook/Reference Book -
ISBN 978-3-527-32636-5 - Wiley-VCH, Weinheim
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Content
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| Short description
The "how to" book for the practising medicinal chemist is ideal for learning and mastering this powerful novel technique. Contains several case studies for the most important scenarios in structure-based lead discovery.
From the contents
Preface
PART I: Principles
VIRTUAL SCREENING OF CHEMICAL SPACE: FROM GENERIC COMPOUND COLLECTIONS TO TAILORED SCREENING LIBRARIES
Introduction
Concepts of Chemical Space
Concepts of Druglikeness and Leadlikeness
Diversity-Based Libraries
Focused Libraries
Virtual Combinatorial Libraries and Fragment Spaces
Databases of Chemical and Biological Information
Conclusions and Outlook
Glossary
PREPARING AND FILTERING COMPOUND DATABASES FOR VIRTUAL AND EXPERIMENTAL SCREENING
Introduction
Ligand Databases
Considering Physicochemical Properties
Undesirables
Property-Based Filtering for Selected Targets
Summary
LIGAND-BASED VIRTUAL SCREENING
Introduction
Descriptors
Search Databases and Queries
Virtual Screening Techniques
Conclusions
THE BASIS FOR TARGET-BASED VIRTUAL SCREENING: PROTEIN STRUCTURES
Introduction
Selecting a Protein Structure for Virtual Screening
Setting Up a Protein Model for vHTS
Summary
Glossary of Crystallographic Terms
PHARMACOPHORE MODELS FOR VIRTUAL SCREENING
Introduction
Compilation of Compounds
Pharmacophore Model Generation
Validation of Pharmacophore Models
Pharmacophore-Based Screening
Postprocessing of Pharmacophore-Based Screening Hits
Pharmacophore-Based Parallel Screening
Application Examples for Synthetic Compound Screening
Application Examples for Natural Product Screening
Conclusions
DOCKING METHODS FOR VIRTUAL SCREENING: PRINCIPLES AND RECENT ADVANCES
Principles of Molecular Docking
Docking-Based Virtual Screening Flowchart
Recent Advances in Docking-Based VS Methods
Future Trends in Docking
PART II: Challenges
THE CHALLENGE OF AFFINITY PREDICTION: SCORING FUNCTIONS FOR STRUCTURE-BASED VIRTUAL SCREENING
Introduction
Physicochemical Basis of Protein-Ligand Recognition
Classes of Scoring Functions
Interesting New Approaches to Scoring Functions
Comparative Assessment of Scoring Functions
Tailoring Scoring Strategies in Virtual Screening
Caveats for Development of Scoring Functions
Conclusion
PROTEIN FLEXIBILITY IN STRUCTURE-BASED VIRTUAL SCREENING: FROM MODELS TO ALGORITHMS
How Flexible Are Proteins? - A Historical Perspective
Flexible Protein Handling in Protein-Ligand Docking
Flexible Protein Handling in Docking-Based Virtual Screening
Summary
HANDLING PROTEIN FLEXIBILITY IN DOCKING AND HIGH-THROUGHPUT DOCKING: FROM ALGORITHMS TO APPLICATIONS
Introduction: Docking and High-Throughput Docking in Drug Discovery
The Challenge of Accounting for Protein Flexibility in Docking
Accounting for Protein Flexibility in Docking-Based Drug Discovery and Design
Conclusions
CONSIDERATION OF WATER AND SOLVATION EFFECTS IN VIRTUAL SCREENING
Introduction
Experimental Approaches for Analyzing Water Molecules
Computational Approaches for Analyzing Water Molecules
Water-Sensitive Virtual Screening: Approaches and Applications
Conclusions and Recommendations
PART III: Applications and Pracitcal Guidelines
APPLIED VIRTUAL SCREENING: STRATEGIES, RECOMMENDATIONS, AND CAVEATS
Introduction
What Is Virtual Screening?
Spectrum of Virtual Screening Approaches
Molecular Similarity as a Foundation and Caveat of Virtual Screening
Goals of Virtual Screening
Applicability Domain
Reference and Database Compounds
Biological Activity versus Compound Potency
Methodological Complexity and Compound Class Dependence
Search Strategies and Compound Selection
Virtual and High-Throughput Screening
Practical Applications: An Overview
LFA-1 Antagonist
Selectivity Searching
Concluding Remarks
APPLICATIONS AND SUCCESS STORIES IN VIRTUAL SCREENING
Introduction
Practical Considerations
Successful Applications of Virtual Screening
Conclusions
PART IV: Scenarios and Case Studies: Routes to Success
SCENARIOS AND CASE STUDIES: EXAMPLES FOR LIGAND-BASED VIRTUAL SCREENING
Introduction
1D Ligand-Based Virtual Screening
2D Ligand-Based Virtual Screening
3D Ligand-Based Virtual Screening
Summary
VIRTUAL SCREENING ON HOMOLOGY MODELS
Introduction
Homology Models versus Crystal Structures: Comparative Evaluation of Screening Performance
Challenges of Homology Model-Based Virtual Screening
Case Studies
TARGET-BASED VIRTUAL SCREENING ON SMALL-MOLECULE PROTEIN BINDING SITES
Introduction
Structure-Based VS for Histone Arginine Methyltransferase PRMT1 Inhibitors
Identification of Nanomolar Histamine H3 Receptor Antagonists by Structure- and Pharmacophore-Based VS
Summary
TARGET-BASED VIRTUAL SCREENING TO ADDRESS PROTEIN-PROTEIN INTERFACES
Introduction
Some Recent PPIM Success Stories
Protein-Protein Interfaces
PPIM's Chemical Space and ADME/Tox Properties
Drug Discovery, Chemical Biology, and In Silico Screening Methods: Overview and Suggestions for PPIM Search
Case Studies
Conclusions and Future Directions
FRAGMENT-BASED APPROACHES IN VIRTUAL SCREENING
Introduction
In Silico Fragment-Based Approaches
Our Approach to High-Throughput Fragment-Based Docking
Lessons Learned from Our Fragment-Based Docking
Challenges of Fragment-Based Approaches
APPENDIX
Software Overview
Virtual Screening Application Studies
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