The first part of this practical guide for industry professionals describes common tools used in the biomolecular simulation of drugs and their targets. A critical analysis of the accuracy of the predictions, the integration of modeling with other experimental data combined with numerous case studies from different therapeutic fields enable users to quickly adopt these new methods for their current projects. The second part then shows how these tools can be applied to drug discovery and development projects. Modeling experts from the pharmaceutical industry and from leading academic institutions present real–life examples for important target classes such as GPCRs, kinases and amyloids as well as for common challenges in structure–based drug discovery.
With its inclusion of novel methods and strategies for the modeling of drug–target interactions in the framework of real–life drug discovery and development, this application–oriented reference is tailor–made for medicinal chemists and those working in the pharmaceutical industry.
Predictive power of biomolecular simulations
Docking by MD
Ligand force fields
Binding free energy predictions based on implicit solvent models
Accuracy of biomolecular simulations
Combination of simulations with experiment
Analysis of simulation data
PART 2: Applications
Molecular dynamics applications in GPCR drug design
Metadynamics–based docking, metadynamics in development of SSR128129E
Inorganic HIV protease inhibitors
Molecular dynamics simulation in virtual screening