FlexS

FlexS predicts the conformation and orientation of one of the ligands relative to the other one. In FlexS the reference-ligand is assumed to be rigid, thus, it should be given in a conformation which is similar to the bound state. The superposition algorithm in FlexS requires only little manual intervention. You can integrate this knowledge into the computations with FlexS by carrying out single steps manually. Thus, FlexS is designed for interactive work on ligand pairs as well as for ligand-based virtual screening. The two main applications of FlexS are ligand super positioning (eg. for CoMFA/QSAR) and virtual screening. If you have a protein and a small molecule binding to it (so called reference-ligand) but no structure of the protein, you can take the reference structure as a negative fingerprint of the active site. FlexS determines the similarity between the test and the reference structure by aligning them. In virtual screening, you have a reference-ligand and a set of compounds and you are interested in prioritizing the compounds for experimental testing.