dockq – DockQ Implementation¶

DockQ(mdl, ref, mdl_ch1, mdl_ch2, ref_ch1, ref_ch2, ch1_aln=None, ch2_aln=None, contact_dist_thresh=5.0, interface_dist_thresh=10.0, interface_cb=False)¶

Computes DockQ for specified interface

DockQ is described in: Sankar Basu and Bjoern Wallner (2016), “DockQ: A Quality Measure for Protein-Protein Docking Models”, PLOS one

Residues are mapped based on residue numbers by default. If you provide ch1_aln and ch2_aln you can enforce an arbitrary mapping.

Parameters:

• mdl (ost.mol.EntityView/ost.mol.EntityHandle) – Model structure

• ref (ost.mol.EntityView/ost.mol.EntityHandle) – Reference structure, i.e. native structure

• mdl_ch1 (str) – Specifies chain in model constituting first part of interface

• mdl_ch2 (str) – Specifies chain in model constituting second part of interface

• ref_ch1 (str) – ref equivalent of mdl_ch1

• ref_ch2 (str) – ref equivalent of mdl_ch2

• ch1_aln (ost.seq.AlignmentHandle) – Alignment with two sequences to map ref_ch1 and mdl_ch1. The first sequence must match the sequence in ref_ch1 and the second to mdl_ch1.

• ch2_aln (ost.seq.AlignmentHandle) – Alignment with two sequences to map ref_ch2 and mdl_ch2. The first sequence must match the sequence in ref_ch2 and the second to mdl_ch2.

• contact_dist_thresh (float) – Residues with any atom within this threshold are considered to be in contact. Affects contact based scores fnat and fnonnat. CAPRI suggests to lower the default of 5.0 to 4.0 for protein-peptide interactions.

• interface_dist_thresh (float) – Residues with any atom within this threshold to another chain are considered interface residues. Affects irmsd. CAPRI suggests to lower the default of 10.0 to 8.0 in combination with interface_cb=True for protein-peptide interactions.

• interface_cb (bool) – Only use CB atoms (CA for GLY) to identify interface residues for irmsd. CAPRI suggests to enable this flag in combination with lowering interface_dist_thresh to 8.0 for protein-peptide interactions.

Returns:

dict with keys nnat, nmdl, fnat, fnonnat, irmsd, lrmsd, DockQ which corresponds to the equivalent values in the original DockQ implementation.