Chemistry Reference
In-Depth Information
3)
Decoy binding and protein structure models.
4)
NMR-derived proximities of ligands to target surface.
5)
Sets of docked poses to derive the interactions required for pose
filtering taking into consideration the prevailing interactions in the
poses and both the receptor and ligand sites.
6)
Pose refinement by global optimization.
7)
Automatic self-organizing map of poses.
8)
Footprint similarity.
9)
Comparative intermolecular analysis.
10)
Free energy calculations.
11)
Weighted-residue profiles.
12)
MD and QM/MM simulation/minimization.
13)
Multiple outputs and rescoring
CHEMICAL LIBRARIES
A number of commercial and public domain chemistry databases (containing from
thousands to millions of compounds) are available. The use of collections of
available compounds is a well-exploited strategy in virtual screening. One route is
to use validated synthetic protocols and available starting materials to prepare
collections of virtual compounds yielding rapid synthesis and structure-activity
relationships.
It would be good if for each compound the following information was included:
1) ionization states at physiological pH, 2) enantiomers and tautomers. 3)
conformers within certain threshold from global minimum energy. It may be also
necessary to filter such computationally demanding databases [479-486].
