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

Proceedings Of The Sixth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Sixth International Conference On Intelligent Systems For Molecular Biology

Contents

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.