Computer-Aided Drug Design Tutorials: Introduction to the Schrodonger Suite
Background
In addition to many academic docking programs, several companies make commercial programs aimed at facilitating drug discovery. Commercial programs are typically aimed at industrial customers who are looking for comprehensive software pacakage that accomplishes many aspects of drug design using a common environment. One very popular software package is the Schrodinger Suite which includes the following major components
- Maestro: graphical uset interface from which most other calculations can be launched
- Macromodel: molecular mechanics-based modeling (minimization, conformational analysis) of bioorganic systems using a variety of force fields
- Jaguar: quantum mechanics software for small molecules; Jaguars are known for their speed
- Prime: predicts three-dimensional structures of proteins, optionally taking into account ligand-induced conformational changes in the protein structure.
- Desmond: highly parallel molecular dynamics simulation program for macromolecules
- QSite: couples Jaguar's QM capabilities with classical molecular mechanics allowing efficient description of chemical reactions in enzyme active sites. The hybrid QM/MM model can also be used for the prediction of binding afinities in cases where classical force fields are unreliable (e.g. significant anisotropic polarization)
- LigPrep: generates and cleans up 3D models of bioorganic molecules. This tool is also able to generate 3D structures of possible tautomers and stereoisomers based on 2D representation of the molecule.
- Phase: facilitates ligand-based drug design by identifying a pharmacophore based on structures of active compounds
- Strike: facilitates ligand-based drug design via quantitative analysis of structure-activity relationships.
- SiteMap: identifies possible binding sites, setting up the target protein for subsequent docking studies
- Glide: docking of ligands into binding pockets in rigid target proteins.
- Induced Fit: Combines the capabilities of Prime and Glide to take into account possible changes in the protein structure upon ligand binding.
- Liaison: predicts ligand binding free energies using the linear interaction approximation