Transient intermolecular interactions drive all biological processes and mediate most normal, pathological, or therapeutic responses. The inherent conformational plasticity of interaction sites is of primary importance because it allows them to accommodate a variety of binding partners; however, it also encumbers prediction or rationalization of these interactions. To promote understanding of flexible transient interactions, we developed the Pocketome (www.pocketome.org), an encyclopedia of experimentally solved conformational ensembles of druggable binding sites in proteins and protein assemblies. The ensemble nature adds an extra, fourth dimension to the otherwise three-dimensional Pocketome data, which is critical for understanding interaction principles and specificity. Pocketome currently contains ~2000 binding site ensembles and is constantly growing. With its unique molecular visualization and analysis tools, Pocketome represents a universal resource for elucidation of principles of transient flexible molecular interactions as well as, in the future, for understanding and predicting ligand specificity and polypharmacology.

Pocketome: An encyclopedia of small-molecule and peptide binding sites in 4D

243rd National Meeting (2012)

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