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To evaluate alignment performance, a web service is also provided to score alignment models against the gold standard using the same metrics reported in the original paper:

  1. To measure how well the bioactive conformation of each ligand has been reproduced (rmsd)
  2. To measure the overall alignment quality by aligning the model to the gold standard using an iterative approach; the percentage of ligands that are correct (<2.0 A) is reported (50% is the objective measure reported in the paper)
  3. To measure the pharmacophoric similarity of the model compared to the gold standard in terms of their FLAPpharm Pharmacophoric Interaction Field similarities.

Alignment models should be submitted as multimol2 files, and the name of the multimol2 file should start with the dataset identifier in addition to any additional user label (for example: P14324_my_alignment_model.mol2).

Each molecule is then assigned to it's experimental equivalent for comparison, using it's InChI identifier, or if this fails by searching for the 4 character pdb code of the experimental structure within the test molecule name.

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