DockTrina is a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation (RMSD) test (see below). Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer.
The DockTrina algorithm is based on fast computation of RMSD. While scanning all possible combinations of pair-wise docking transforms, a tetramer of chains \(A\), \(B\), \(C\) and \(A’\) is formed. Here \(A’\) is an image of \(A\), obtained with the net transform \(T^{AA}\) :\[T^{AA} = T^{AB} \cdot T^{BC} \cdot T^{CA} \] \[A’ = T^{AA} \cdot A\] If the individual pair-wise transforms are perfectly mutually consistent, then chain \(A\) should be transformed into itself. It means that RMSD between chains \(A\) and \(A’\) characterizes the quality of a trimeric prediction. We use the RigidRMSD library to perform each RMSD test in constant time, which makes DockTrina fast and efficient tool to predict triangular trimers.
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Linux Fedora 14 x64
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Linux Fedora 14 x32
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Mac OS X 10.6
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Benchmark
DockTrina was tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. The bound benchmark includes 85 proteins with crystallographic symmetry, 76 protein complexes related by noncrystallographic symmetry (NCS), and 59 nonsymmetrical protein complexes. The unbound benchmark consists of seven complexes, three of which possess threefold crystallographic symmetry.
Bound Benchmark NCS Set
Bound Benchmark Nonsymmetrical Set
Unbound Benchmark Set
Each benchmark contains three chains constituting a trimer, three dimers taken from a trimer and whole trimer complex in PDB format. Please, cite this article, when using these benchmarks in your research.
Examples
1M1J example (input PDB files + pair-wise transforms produced by Hex + Hex input template) DockTrina example 1M1J.
Hex can be obtained separately at http://hex.loria.fr.
Type in the command line:
1J34 example (input PDB files + pair-wise transforms produced by Hex + Hex input template) DockTrina example 1J34.
Type in the command line:
1EUW symmetric example (input PDB files + pair-wise transforms produced by Hex + Hex input template) DockTrina example 1EUW.
Type in the command line:
