The Global Range Molecular Matching (GRAMM) methodology is an empirical approach to smoothing the macromolecular energy function by changing the range of the atom-atom potentials. The technique allows to locate the area of the global minimum of intermolecular energy for structures of different accuracy. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The procedure performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules. The molecular pairs may be: two proteins, a protein and a smaller compound, two transmembrane helices, etc. GRAMM may be used for high-resolution molecules (high-resolution docking), for inaccurate structures, where only the gross structural features are known, and in cases of large conformational changes (low-resolution docking). The high-resolution docking is designed for accurate complex predictions, in case of small structural inaccuracies. The low-resolution docking is designed for the prediction of the gross features of a complex, in case of major structural inaccuracies. It may also be used, for the accurate structures, to overcome the multiminima problem, or to reveal the role of large-scale structural factors in the formation of protein complexes.
 

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