Installation
Clone the repository, then install the necessary libraries with pip:
git clone https://github.com/bjornwallner/DockQ/
cd DockQ
pip install .
Quick start for two interacting partners (two-chain-models) run with:
DockQ <model> <native>
Example
bash$ DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.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 *
* Ref: S. Basu and B. Wallner, DockQ: A quality measure for *
* protein-protein docking models *
* doi:10.1371/journal.pone.0161879 *
* For comments, please email: [email protected] *
****************************************************************
Model : examples/1A2K_r_l_b.model.pdb
Native : examples/1A2K_r_l_b.pdb
Total DockQ over 3 native interfaces: 1.959
Native chains: A, B
Model chains: B, A
DockQ_F1: 0.996
DockQ: 0.994
irms: 0.000
Lrms: 0.000
fnat: 0.983
Native chains: A, C
Model chains: B, C
DockQ_F1: 0.567
DockQ: 0.511
irms: 1.237
Lrms: 6.864
fnat: 0.333
Native chains: B, C
Model chains: A, C
DockQ_F1: 0.500
DockQ: 0.453
irms: 2.104
Lrms: 8.131
fnat: 0.500
Help page
bash$ DockQ -h
usage: DockQ [-h] [--capri_peptide] [--short] [--verbose] [--use_CA] [--no_align] [--optDockQF1] [--allowed_mismatches ALLOWED_MISMATCHES] [--mapping MODELCHAINS:NATIVECHAINS]
<model> <native>
DockQ - Quality measure for protein-protein docking models
positional arguments:
<model> path to model file
<native> path to native file
optional arguments:
-h, --help show this help message and exit
--capri_peptide use version for capri_peptide (DockQ cannot not be trusted for this setting)
--short short output
--verbose, -v talk a lot!
--use_CA, -ca use CA instead of backbone
--no_align Do not align native and model using sequence alignments, but use the numbering of residues instead
--optDockQF1 optimize on DockQ_F1 instead of DockQ
--allowed_mismatches ALLOWED_MISMATCHES
number of allowed mismatches when mapping model sequence to native sequence.
--mapping MODELCHAINS:NATIVECHAINS
Specify a chain mapping between model and native structure. If the native contains two chains "H" and "L" while the model contains two chains "A" and "B",
and chain A is a model of native chain H and chain B is a model of native chain L, the flag can be set as: '--mapping AB:HL'. This can also help limit the
search to specific native interfaces. For example, if the native is a tetramer (ABCD) but the user is only interested in the interface between chains B and
C, the flag can be set as: '--mapping :BC' or the equivalent '--mapping *:BC'.