Name
Title | ||
|---|---|---|
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. |
Abstract | ||
|---|---|---|
Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon-alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein-protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein-protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models. |
Year | DOI | Venue |
|---|---|---|
2017 | 10.1093/bib/bbw027 | BRIEFINGS IN BIOINFORMATICS |
Keywords | Field | DocType |
template-based modeling,interface restrained docking,CA-CA-guided docking,AIR-guided docking,refinement | Pairwise comparison,Lead Finder,Biology,Docking (dog),Searching the conformational space for docking,Protein–ligand docking,Protein protein,Template,Bioinformatics | Journal |
Volume | Issue | ISSN |
18 | 3 | 1467-5463 |
Citations | PageRank | References |
1 | 0.35 | 6 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Li Xue | 1 | 24 | 1.63 |
| João P. G. L. M. Rodrigues | 2 | 16 | 2.63 |
| Drena Dobbs | 3 | 423 | 35.43 |
| Vasant Honavar | 4 | 3353 | 468.10 |
| Alexandre M. J. J. Bonvin | 5 | 41 | 7.08 |