The user uploads the same receptor and ligand structures that have been used for docking and the docking results files in the field + Docking files. User can specify the names for the receptor and ligand, but can also leave these fields blank. Docking results generated by the following servers are accepted as QASDOM input without any additional preprocessing
Cut-off distance for interatomic contacts, which define a contact in QASDOM can be changed, by default this value is 4.5 Å. Plausible values range from 4 to 6 Å.
Generally, any models of complexes that adhere to the PDB format, archived with zip, tar, tar.gz, gz or without archiving are also accepted. Molecules of receptor and ligand with various chemical structures can be present, including proteins and nucleic acids. Chemical modifications are also allowed. QASDOM compares the sequence of receptor and ligand structures submitted by the user and those present in the docking files, so it is important that these molecules are the same.
The main results page displays the models ranking table that includes Sm and Smatomic scores, and the numbers of residue contacts (RC) and atomic contacts (RC Atomic). The table also shows structural cluster number and chain ID for each model. On the right, a 3D visualization window displays all models of the uploaded dataset, with ligands coloured according to their structural clusters, which can be identified by their chain ID. Table rows provide links allowing to display the selected model in the interactive 3D structure viewer, and the links that open structural clusters in a new window. The user can rotate a structure with the left mouse button, and by pointing the mouse cursor can display chain ID, the name and number of the highlighted amino acid residue. Ligand chain IDs corresponds to the cluster IDs in the table.
Further down on the results page there are graphs showing atomic and residue contacts in the sequence for the dataset of models. Graphs show receptor and ligand separately.
Red line shows the median for each graph.
By clicking on a bar in the graph, the user is redirected to the page listing all models with contacts in this residue (sequence position).
The user can view each model in the viewer window by clicking the View link, and download each model separately or all models as an archive.
QASDOM description is available here.