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Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection

  • Flavio Ballante
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1824)

Abstract

Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.

Key words

Drug design Drug discovery Molecular docking Molecular modeling Docking assessment Structure-based drug design (SBDD) 

Notes

Acknowledgments

F.B. thanks Prof. Garland R. Marshall (Washington University School of Medicine in St. Louis, MO) for supporting and funding the design and development of the Clusterizer-DockAccessor protocol; Dr. Chris M. W. Ho (Drug Design Methodologies, LLC, St. Louis, MO) and Ms. Mariama Jaiteh (Uppsala University, Uppsala, Sweden) for providing insightful comments.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisUSA
  2. 2.Department of Cell and Molecular BiologyUppsala Biomedicinska Centrum BMC, Uppsala UniversityUppsalaSweden

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