Computational Analysis of

Protein Interactions

Ilya A. Vakser

Assistant Professor of Pharmacology 
Department of Cell and Molecular Pharmacology 
Medical University of South Carolina 


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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