A Computational System for Modeling Flexible Protein-Protein and Protein-DNA Docking

J. E Sternberg, Patrick Aloy, Henry A. Gabb, Richard M. Jackson, Gidon Moont, Enrique Querol, Francesc X Aviles

A computational system is described that predicts the structure of protein/protein and protein/DNA complexes starting from unbound coordinate sets. The approach is (i) a global search with rigid-body docking for complexes with shape complementarity and favourable electrostatics; (ii) use of distance constraints from experimental ( or predicted) knowledge of critical residues; (iii) use of pair potential to screen docked complexes and (iv) refinement and further screening by protein-side chain optimisation and interfacial energy minimisation. The system has been applied to model ten protein/ protein and eight protein-repressor / DNA (steps i to iii only) complexes. In general a few complexes, one of which is close to the true structure, can be generated.

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