Table 1 Comparison scores in OpenStructure and their applications

From: A fully automated benchmarking suite to compare macromolecular complexes

 

Protein tertiary structures

RNA tertiary structures

Protein complexes

Protein–RNA complexes

Small molecules

Chain mapping4

Primary citation

LDDT/bb-LDDT1

Yes

Yes

Yes

Yes

No

QSMap

Ref. 36 and updates in this manuscript

i-LDDT1

No

No

Yes

Yes

No

QSMap

This manuscript

QS-score1

No

No

Yes

No

No

QSMap

Ref. 28

DockQ/ fnat/ i-RMSD./ L-RMSD2

No

No

Yes

Yes

No

QSMap

Ref. 37

ICS/IPS2,5

No

No

Yes

Yes

No

QSMap

Ref. 6

DockQ-ave/DockQ-wave1

No

No

Yes

No

No

QSMap

Ref. 57

GDT2

Yes

Yes

Yes

Yes

No

QSMapR

Ref. 33

r.m.s.d.2

Yes

Yes

Yes

Yes

No

QSMapR

Ref. 32

CAD-score3

Yes

Yes

Yes

Yes

No

QSMap

Ref. 35

TM-score3

Yes

Yes

Yes

Yes

No

US-align

Ref. 25

BiSyRMSD1

No

No

No

No

Yes

Full enumeration of binding site chains

This manuscript

LDDT-PLI1

No

No

No

No

Yes

Full enumeration of binding site chains

This manuscript

  1. 1The OpenStructure scoring framework is the reference implementation.
  2. 2Implementation in the OpenStructure scoring framework—implementation details available in Methods and comparison to reference implementation available in Supplementary Section 4.
  3. 3External tool integrated in the OpenStructure scoring framework.
  4. 4Only relevant for protein complexes or protein–RNA complexes, external tools either use their own chain mapping or the OpenStructure chain mapping gets injected.
  5. 5Scores for higher order oligomers may differ from legacy implementation used until CASP15, with differences discussed in Methods.
Back to article page