Overview
DockRank is a tool to rank protein-protein docked models based on predicted partner-specific protein interface residues.
DockRank uses
PS-HomPPI to predict the partner-specific protein interface residues for the docked model. By comparing the predicted interfaces and the interfaces in the docked models, DockRank gives a rank
for the docked models. The models with high interface similarity with the predicted interfaces are ranked top.
DockRank takes the PDB formatted files of the docked models as input.
Output
DockRank will output the ranking score for each docked model based on the similarity of predicted interfaces and the interfaced in the docked models. DockRank will also output the interface prediction results from PS-HomPPI.
Running Time: The estimated running time is 6 seconds per PDB files.
Our interface prediction PS-HomPPI is a homo-interolog (homologous interacting proteins) based method. To achieve an objective evaluation of DockRank, user may provide a list of PDB IDs (potential bound complexes of docked models) to be removed from homo-interologs used by the interface predictor PS-HomPPI.
The relative solvent accessible area (RASA) Threshold RASA threshold is to determine a protein residue a surface residue or not. Surface residues are regarded as residues that have RASA at least RASA threshold.
Atom distance Threshold Atom distance threshold is to determine a surface residue an interface residue or not. An interface residue is a surface residue that has at least one atom is within Atom distance threshold from any atoms of residues in another protein chain.
K in K-nearest homologs K is the parameter for PS-HomPPI interface predictor. PS-HomPPI predicts interface residues in a query protein based on the known interface residues of its K closest homologous interacting pairs in the alignment.
Weight of predicted interface from different Zones PS-HomPPI predicts interface residues for each pair of chains in the docked models. For each query chain pair, PS-HomPPI searches for homo-interologs (homologous interacting proteins), and transfers the interfaces of homo-interologs to the query chain pair. Based on the sequence similarity between the query pair and the homo-interologs, homo-interologs are regarded from four different zones: Safe Zone, Twilight Zone 1, Twilight Zone 2, and Dark Zone. The interface transfer from homo-interologs in the Safe Zone tends to be most reliable. The reliability of interface transfer decreases from Safe Zone, to Twilight Zone 1, to Twilight Zone 2, and to Dark Zone. When one docked model contains more than two chains, it is possible that differnt chain pairs in one docked model may have homo-interologs from different Zones. DockRank allows the users to give different weight to the predicted interfaces derived from homo-interologs in differnt Zones.
Note: DockRank only use the predicted interfaces between receptor and ligand to rank docked models.
