Abstract
Biological receptors are not completely rigid molecules. They can adopt many different structures at physiologically relevant temperatures. Different drugs can bind to different ensembles of conformations of these receptors. Reliably predicting to which conformations of a receptor a compound might bind well calls for the proper account of receptor flexibility. Researchers have developed various computational methods to deal with this aspect of drug discovery. Some of these methods are still too expensive to be used extensively in practice. Ensemble docking has emerged as one of the most popular practical approaches. This chapter summarizes basic principles and common techniques underlying ensemble docking, illustrates its use with several examples, and concludes with suggestions for future improvements.
Original language | American English |
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Journal | Computer-Aided Drug Discovery |
DOIs | |
State | Published - Jan 1 2015 |
Keywords
- Boltzmann-enhanced discrimination of receiver operating characteristics (BEDROC)
- Computer-aided drug design
- Conformational transition paths
- Enrichment factor
- Ensemble docking
- Homology modeling
- Molecular dynamics
- Normal mode
- Virtual screening
Disciplines
- Biology
- Medicinal-Pharmaceutical Chemistry