DockQ: A quality measure for PPI complexes based on CAPRI evaluation protocol
Requires a fortran90 compiler (prefered: ifort)
Installation
git clone https://github.com/nemo8130/DockQ-fortran-code
cd DockQ-fortran-code/DockQ
./install.bash <fortran90-compiler> (Default: ifort)
Run with
./DockQ.exe <model> <native>
Example
bash$ ./DockQ.exe ./EXAMPLE_PDBS/model.pdb ./EXAMPLE_PDBS/native.pdb
-
DockQ * - Scoring function for protein-protein docking models *
- Statistics on CAPRI data: *
- 0.00 <= DockQ < 0.23 - Incorrect *
- 0.23 <= DockQ < 0.49 - Acceptable quality *
- 0.49 <= DockQ < 0.80 - Medium quality *
-
DockQ >= 0.80 - High quality * - Reference: Sankar Basu and Bjorn Wallner, DockQ:... *
- For comments, please email: bjornw@ifm.liu.se *
Number of equivalent residues at the interface: 103 (receptor: A) 88 (ligand: B)
<=== defined at an all-atom atomic cutoff of 10.00 Å (iRMS) ===>
fnat: 0.533: 32 correct out of 60 native contacts at the receptor-ligand interface
fnonat: 0.238: 10 non-native out of 42 model contacts at the receptor-ligand interface
Fnat= 0.533 LRMS_bb= 1.516 IRMS= 1.197 DockQ= 0.70442
CAPRI_class (fnat, iRMS, LRMS): Medium
CAPRI_class (DockQ) : Medium
outfile: fort.245
rename the outfile as you wish