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Consensus scoring for enriching near-native structures from protein-protein docking decoys
Shide Liang1, Samy O Meroueh, Guangce Wang
1Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, USA.
Proteins
|October 3, 2008
Summary
Identifying near-native protein complexes is challenging. A new consensus scoring function, ENDES, significantly enriches these structures by combining energy, conservation, and interface propensity scores.
Area of Science:
- Computational Biology
- Structural Biology
- Biophysics
Background:
- Accurate prediction of protein-protein complexes is crucial in structural biology.
- Identifying near-native protein docking decoys among numerous false positives remains a significant challenge.
- Existing scoring functions often struggle to effectively rank correct protein complex models.
Purpose of the Study:
- To develop and evaluate a novel consensus scoring function, ENDES, for enriching near-native protein-protein complex decoys.
- To improve the success rate of detecting biologically relevant protein-protein interactions from computational docking.
- To integrate energy, conservation, and interface propensity scores for enhanced decoy ranking.
Main Methods:
- Modification and combination of energy, conservation, and interface propensity scoring functions.
- Development of the ENDES (ENergy, DEtection, Scoring) consensus scoring function.
- Testing ENDES on the ZDOCK2.3 and Benchmark 2.0 decoy sets.
Main Results:
- Individual scoring functions showed enrichment for most protein complex targets.
- The interface propensity score demonstrated the highest enrichment among the individual scores.
- The ENDES consensus score significantly increased the enrichment of near-native structures, improving ranking by approximately six-fold on average.
- ENDES successfully reduced 2000 decoys to 200, substantially increasing the fraction of near-native structures.
Conclusions:
- The ENDES consensus scoring function effectively enriches near-native protein-protein complex decoys.
- Combining multiple scoring criteria enhances the accuracy of protein docking predictions.
- ENDES provides a valuable tool for identifying biologically relevant protein-protein interactions and is available as a downloadable program.
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