Loading...
Please wait, while we are loading the content...
Similar Documents
Docking by structural similarity at protein-protein interfaces (2008)
| Content Provider | CiteSeerX |
|---|---|
| Author | Sinha, Rohita Kundrotas, Petras J. Vakser, Ilya |
| Abstract | Rapid accumulation of experimental data on protein-protein complexes drives the paradigm shift in protein docking from ‘traditional, ’ template free approaches to template based techniques. Homology docking algorithms based on sequence similarity between target and template complexes can account for up to 20 % of known protein-protein interactions. When highly homologous templates for the target complex are not available, but the structure of the target monomers is known, docking by local structural alignment may provide an adequate solution. Such an algorithm was developed based on the structural comparison of monomers to co-crystallized interfaces. A library of the interfaces was generated from co-crystallized protein-protein complexes in PDB. The partial structure alignment algorithm was validated on the DOCKGROUND benchmark sets. The optimal performance of the partial (interface) structure alignment was achieved with the interface residues defined by 12Å distance across the interface. Overall, the partial structural alignment yielded more accurate models than the full structure alignment. Most templates identified by the partial structural alignment had low sequence identity to the target, which makes them hard to detect by sequence-based methods. The results indicate that the structure alignment techniques provide a much needed addition to the docking arsenal, with the combined structural alignment and template free docking success rate significantly surpassing that of the free docking alone. |
| File Format | |
| Publisher Date | 2008-01-01 |
| Access Restriction | Open |
| Subject Keyword | Structural Similarity Protein-protein Interface Partial Structural Alignment Interface Residue Combined Structural Alignment Paradigm Shift Rapid Accumulation Template Complex Target Monomer Protein-protein Complex Sequence Similarity Dockground Benchmark Set Local Structural Alignment Low Sequence Identity Homologous Template Structure Alignment Technique Co-crystallized Protein-protein Complex Co-crystallized Interface Structural Comparison Full Structure Alignment Optimal Performance Template Free Approach Structure Alignment Success Rate Partial Structure Alignment Algorithm Protein-protein Interaction Target Complex Sequence-based Method Adequate Solution Experimental Data Accurate Model |
| Content Type | Text |
