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Main description:
This volume covers the techniques necessary for a successful fragment-based drug design project, beginning from defining the problem in terms of preparing the protein model, identifying potential binding sites, and the consideration of various candidate fragments for simulation. The second part discusses the technical aspects that various methods have used to simulate fragment binding to a target protein by using Monte Carlo, molecular dynamics, and docking algorithms. After simulations, fragments are assembled into molecules using a variety of approaches, which are explored next. A discussion of design strategies and consideration of drug-like properties is included as part of the design process at this stage. Finally, several examples of successful fragment-based drug design projects are presented. Written for the Methods in Molecular Biology series, this work contains the kind of detailed description and implementation advice to encourage success in the lab.
Practical and cutting-edge, Fragment-Based Methods in Drug Discovery takes into account the great accomplishments in the field to provide an ideal guide for researchers continuing to investigate this exciting area of pharmacological study.
Contents:
Part I: Preparation
1. Solvation Methods for Protein-Ligand Docking
Rachelle J. Bienstock
2. Binding Site Druggability Assessment in Fragment-Based Drug Design
Yu Zhou and Niu Huang
3. Generating "Fragment-Based Virtual Library" Using Pocket Similarity Search of Ligand-Receptor Complexes
Raed S. Khashan
4. Virtual Fragment Preparation for Computational Fragment-Based Drug Design
Jennifer L. Ludington
5. Fragment Library Design: Using Cheminformatics and Expert Chemists to Fill Gaps in Existing Fragment Libraries
Peter S. Kutchukian, Sung-Sau So, Christian Fischer, and Chris L. Waller
Part II: Simulation
6. Protocol for Fragment Hopping
Kevin B. Teuscher and Haitao Ji
7. Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design
Christina E. Faller, E. Prabhu Raman, Alexander D. MacKerell, Jr., and Olgun Guvench
8. A Computational Fragment-Based De Novo Design Protocol Guided by Ligand Efficiency Indices (LEI)
Alvaro Cortes-Cabrera, Federico Gago, and Antonio Morreale
9. Scoring Functions for Fragment-Based Drug Discovery
Jui-Chih Wang and Jung-Hsin Lin
Part III: Design
10. Computational Methods for Fragment-Based Ligand Design: Growing and Linking
Rachelle J. Bienstock
11. Design Strategies for Computational Fragment-Based Drug Design
Zenon D. Konteatis
12. Protein Binding Site Analysis for Drug Discovery Using a Computational Fragment-Based Method
Jennifer L. Ludington
Part IV: Case Studies
13. Fragment-Based Design of Kinase Inhibitors: A Practical Guide
Jon A. Erickson
14. Designing a Small Molecule Erythropoietin Mimetic
Frank Guarnieri
15. Designing an Orally Available Non-Toxic p38 Inhibitor with a Fragment-Based Strategy
Frank Guarnieri
PRODUCT DETAILS
Publisher: Springer (Humana Press Inc.)
Publication date: February, 2015
Pages: 230
Weight: 6542g
Availability: Available
Subcategories: Pharmacology
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