Features:

• Considers ligand-based and docking-based virtual screens and the challenges facing the field
• Discusses choice of compounds that are best suited as drug leads
• Includes descriptor-based similarity, traditional pharmacophore searching, and similarity based on three-dimensional-pharmacophore fingerprints
• Discusses practical considerations of molecular docking

Virtual Screening in Drug Discovery does not overwhelm you with more information than you need. Many of the strategies outlined will transcend the specifics of any given method.

Virtual Screening in Drug Discovery does not proclaim to offer single best ways to use the programs. What it does is provide a snapshot of virtual screening that gives you easy access to strategies and techniques for lead discovery.

Part I offers perspectives on both ligand-based and docking-based virtual screens. The authors of these chapters frame many of the challenges currently facing the field. Part II considers the choice of compounds that are best suited as drug leads. Part III discusses ligand-based approaches, including descriptor-based similarity, traditional pharmacophore searching, and similarity based 3D-pharmacophore fingerprints. The final two sections are devoted to molecular docking. Part IV outlines some important and practical considerations relating to the energetics of protein-ligand binding and target-site topography, whereas specific docking algorithms and strategies are discussed in Part V.

Contents

Perspectives on Virtual Screening

• Virtual Screening: Scope and Limitations
• Addressing the Virtual Screening Challenge-The Flex* Approach
• An Analysis of Critical Factors Affecting Docking and Scoring

Compound and Hit Suitability for Virtual Screening

• Compound Selection for Virtual Screening
• Experimental Identification of Promiscuous

Ligand-based Virtual Screening Approaches

• Data Mining Approaches for Enhancement of Knowledge-Based Content of De Novo Chemical Libraries
• Pharmacophore-Based Virtual Screening: A Practical Perspective
• Using Pharmacophore Multiplet Fingerprints for Virtual HTS

Important Considerations Impacting Molecular Docking

• Potential Functions for Virtual Screening and Ligand Binding Calculations: Some Theoretical Considerations
• Solvation-Based Scoring for High-Throughput Docking
• Classification of Ligand-Receptor Complexes Based on Receptor Binding Site Characteristics

Docking Strategies and Algorithms

• A Practical Guide to DOCK 5
• Pharmacophore-Based Molecular Docking: A Practical Guide
• Fragment Based High Throughput Docking
• Protein-Ligand Docking and Virtual Screening With GOLD
• A Brief History of Glide: A New Paradigm for Docking and Scoring in Virtual Screening

Index

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