What is the GNM DB? Which questions can be answered?
Several studies in the last decade have drawn attention to the significance of intrinsic dynamics as a major determinant of the mechanism of action of proteins and their complexes (1-5). Intrinsic dynamics refers to conformational changes intrinsically favored by 3D structure, which often underlie the adaptation of biomolecules to functional interactions (6). As a consequence, an important question is to assess which structural elements (e.g. residues, secondary structures, domains, or entire subunits ) undergo large fluctuations away from their mean positions (i.e. those enjoying high mobility), or which ones provide adequate flexibility to enable conformational changes (e.g. hinge-bending sites) that may be relevant to function. Furthermore, it is often of interest to determine which structural elements are subject to strongly correlated (or anticorrelated) motions, toward gaining insights into allosterically coupled regions. The GNM (7, 8) addresses these questions. It further allows to dissect these properties into the contributions of individual modes, thus elucidating the cooperative (global) couplings (cross-correlations) underlied by low frequency modes. For more information see Theory and Tutorial.