Docking Protein Domains Using Contact Maps
Author Information
Author(s): Lise Stefano, Walker-Taylor Alice, Jones David T
Primary Institution: University College London
Hypothesis
The real configuration of contacts is the one that maximizes the score assigned by a scoring function combining structural, physicochemical, and evolutionary information.
Conclusion
Contact docking appears feasible and able to complement other computational methods for predicting protein-protein interactions.
Supporting Evidence
- The method correctly predicts some contacts between protein domains.
- Predicted residues tend to be significantly closer to each other than random pairs.
- Predicted contacts can discriminate the best model among a set of optimal solutions.
Takeaway
The study presents a new way to predict how protein parts fit together by looking at which parts are likely to touch each other.
Methodology
The method uses a scoring function based on contact maps and a simulated annealing algorithm to predict contacting residues between protein domains.
Limitations
The method does not produce a 3D complex directly and may not correspond to physically realizable conformations.
Digital Object Identifier (DOI)
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