Fig. 1.

Schematic representation of the Flexi-pharma protocol for one test molecule. First, an MD simulation is performed. Then, a set of pharmacophores is determined for each MD conformation of the receptor. Then, Pharmer [34] is used to identify if the molecule matches any pharmacophore from each MD conformation; if so, a vote is given to the molecule. Finally, we sum the votes from the set of MD conformations. The green, blue, red and gray circles are hydrophobic, H-bond donor, H-bond acceptor and aromatic features, respectively