New benchmark metrics for protein-protein docking methods

By Mu Gao, Jeffrey Skolnick. 2011

44 citations recorded by the source corpus.

With the development of many computational methods that predict the structural models of protein‐protein complexes, there is a pressing need to benchmark their performance. As was the case for protein monomers, assessing the quality of models of protein complexes is not straightforward. An effective scoring scheme should be able to detect substructure similarity and estimate its statistical significance. Here, we focus on characterizing the similarity of the interfaces of the complex and introduce two scoring functions. The first, the interfacial Template Modeling score (iTM‐score), measures the geometric distance between the interfaces, while the second, the Interface Similarity score (IS‐score), evaluates their residue‐residue contact similarity in addition to their geometric similarity. We first demonstrate that the IS‐score is more suitable for assessing docking models than the iTM‐score. The IS‐score is then validated in a large‐scale benchmark test on 1562 dimeric complexes. Finally, the scoring function is applied to evaluate docking models submitted to the Critical Assessment of Prediction of Interactions (CAPRI) experiments. While the results according to the new scoring scheme are generally consistent with the original CAPRI assessment, the IS‐score identifies models whose significance was previously underestimated. Proteins 2011. © 2011 Wiley‐Liss, Inc.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Björn Wallner
2. Sankar Basu
3. Arne Elofsson
4. Isak Johansson-Åkhe
5. Bruno E. Correia
6. Freyr Sverrisson

In Materials Chemistry

1. Björn Wallner
2. Sankar Basu
3. Arne Elofsson
4. Liam J. McGuffin

In Molecular Biology

1. Björn Wallner
2. Sankar Basu
3. Arne Elofsson
4. Liam J. McGuffin
5. Riviera Maya
6. Erik Lindahl
7. Torsten Schwede
8. Karolis Uziela

Citations in the corpus

• DockQ: A Quality Measure for Protein-Protein Docking Models (2016, background): “…where there are several widely accepted quality measures; e.g., C α -RMSD, GDT_TS [3], MaxSub [4], TM-score [5], and S-score [6], the IS-score [7] for assessing protein complex models has not achieved wide adoption by the field and the current state of the art evaluation protocol for…”
• Finding correct protein–protein docking models using ProQDock (2016, unknown): “DockQ is a score between 0 and 1, which is similar to IS-score (Gao and Skolnick, 2011) in its design, but optimized to reproduce the CAPRI classification (Lensink et al.”