Software
QuasarX
The quasi-atomistic receptor modeling software Quasar is a genuine 6D-QSAR tool which explicitly allows for induced fit — the structural adaptation of the protein to the topology of a ligand molecule. In Quasar, the fourth dimension refers to the possibility to represent each ligand molecule by an ensemble of conformations, orientations or protonation states, thereby reducing the bias associated with ligand alignment. The fifth dimension refers to a multiple representation of induced-fit models while the sixth dimension allows for the simultaneous evaluation of different solvation scenarios. Other features include the H-bond flip-flop property, the consideration of entropic and solvation effects as well as the underlying directional force field. A family of quasi-atomistic receptor models is generated using a genetic algorithm combined with weighted cross-validation. The functional-group analysis option allows to decompose the (calculated) free energy of ligand binding into contributions from the individual functional groups defining a ligand molecule — thereby allowing for a rational optimization of the desired molecular properties.
Current version: 6.1
Authors: Angelo Vedani and Max Dobler
Computer platforms: Mac OS X, Linux, Windows
References:
- ChemMedChem. 2010, 5, 2088–2101 View abstract
- ChemMedChem. 2009, 4, 100–109 View abstract
- ChemMedChem. 2007, 2, 78–87 View abstract
- J. Med. Chem. 2005, 48, 3700–3703 View abstract
- J. Med. Chem. 2005, 48, 1515–1527 View abstract
- J. Med. Chem. 2002, 45, 2139–2149 View abstract
- J. Med. Chem. 2000, 43, 4416–4427 View abstract
- J. Am. Chem. Soc. 1998, 120, 4471–4477 View abstract