Exit Regions of Cavities in Proteins Proteins have a complex three dimensional structure with empty cavities and tunnels in the interatomic space and these spatial features are often essential for the correct biological function. Many discrete and analytical methods have been developed for the computation, analysis and visualization of these features. In this paper, we focus on the connection of cavities with the space outside a protein. This connection would normally be described by tunnels. However, the number of possible solutions can be very high and therefore a nontrivial pruning of solutions is needed to deliver only a few representatives. Therefore, we propose an alternative kind of spatial features called exit regions of cavities. These regions capture the critical locations where a spherical probe, initially placed in a cavity, can leave the protein if the probe is allowed to shrink. The shape of an exit region is more detailed when compared against the simple circular profile of a tunnel. Tunnels, on the other hand, provide more information about the exact path.

Matching of EM Map Segments to StructurallyRelevant Biomolecular Regions Electron microscopy is a technique used to determine the structure of biomolecular machines via threedimensional images (called maps). The stateoftheart is able to determine structures at resolutions that allow us to identify up to secondary structural features, in some cases, but it is not widespread. Furthermore, because molecular interactions often require atomiclevel details to be understood, it is still necessary to complement current maps with techniques that provide finergrain structural details. We applied segmentation techniques to maps in the Electron Microscopy Data Bank (EMDB), the standard community repository for these data. We assessed the potential of these algorithms to match functionally relevant regions in their atomicresolution image counterparts by comparing against three protein systems, each with multiple atomicdetailed domains. We found that at least 80% of amino acid residues in 7 out of 12 domains were assigned to single segments, suggesting there is potential to match the lower resolution segmented regions to the atomic counterparts. We also qualitatively analyzed the potential on other EMDB structures, as well as generating the raw segmentation information for the complete EMDB, for interested researchers to use. Results can be accessed online and the library developed is provided as part of an opensource project.