DockTrina

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.

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tetramer-01.jpgThe 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.

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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:

docktrina -fA 1M1J_A.pdb -fB 1M1J_B.pdb -fC 1M1J_C.pdb -trAB 1M1J_AB_transform.txt -trBC 1M1J_BC_transform.txt -trCA 1M1J_CA_transform.txt -trAC 1M1J_AC_transform.txt -trCB 1M1J_CB_transform.txt -trBA 1M1J_BA_transform.txt -N 100 -o top10.pdb

1J34 example (input PDB files + pair-wise transforms produced by Hex + Hex input template) DockTrina example 1J34.
Type in the command line:

docktrina -fA 1J34_A.pdb -fB 1J34_B.pdb -fC 1J34_C.pdb -trAB 1J34_AB_transform.txt -trBC 1J34_BC_transform.txt -trCA 1J34_CA_transform.txt -trAC 1J34_AC_transform.txt -trCB 1J34_CB_transform.txt -trBA 1J34_BA_transform.txt -N 1000 -o top10.pdb

1EUW symmetric example (input PDB files + pair-wise transforms produced by Hex + Hex input template) DockTrina example 1EUW.
Type in the command line:

docktrina -m 1EUW_A.pdb -tr 1EUW_AB_transform.txt -N 100 -o out.pdb

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