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- Multi-GPU-Based Detection of Protein Cavities using Critical PointsPublication . Dias, Sérgio; Nguyen, Quoc; Jorge, Joaquim A; Gomes, AbelProtein cavities are specific regions on the protein surface where ligands (small molecules) may bind. Such cavities are putative binding sites of proteins for ligands. Usually, cavities correspond to voids, pockets, and depressions of molecular surfaces. The location of such cavities is important to better understand protein functions, as needed in, for example, structure-based drug design. This article introduces a geometric method to detecting cavities on the molecular surface based on the theory of critical points. The method, called CriticalFinder, differs from other surface-based methods found in the literature because it directly uses the curvature of the scalar field (or function) that represents the molecular surface, instead of evaluating the curvature of the Connolly function over the molecular surface. To evaluate the accuracy of CriticalFinder, we compare it to other seven geometric methods (i.e., LIGSITE-CS, GHECOM, ConCavity, POCASA, SURFNET, PASS, and Fpocket). The benchmark results show that CriticalFinder outperforms those methods in terms of accuracy. In addition, the performance analysis of the GPU implementation of CriticalFinder in terms of time consumption and memory space occupancy was carried out.
- GPU-Based De- tection of Protein Cavities using Gaussian SurfacesPublication . Dias, Sérgio; Martins, Ana Mafalda; Nguyen, Quoc; Gomes, AbelProtein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding cavities as aggregates of grid nodes outside the molecule, under the condition that such cavities are bracketed by nodes on the molecule surface along a set of directions (not necessarily aligned with coordinate axes). Therefore, these methods are sensitive to scanning directions, a problem that we call cavity ground-and-walls ambiguity, i.e., they depend on the position and orientation of the protein in the discretized domain. Also, it is hard to distinguish grid nodes belonging to protein cavities amongst all those outside the protein, a problem that we call cavity ceiling ambiguity.
- A new tool for network analysis on team sportsPublication . Silva, Frutuoso; Nguyen, Quoc; Gomes, Abel; Martins, Fernando; Clemente, Filipe ManuelNetwork analysis has been used to classify the interactions between teammates in team sports. However, no dedicated software or application was specifically developed to import, compute and export data in the specific case of sports, as far as we know. Based on that, we intend to propose a new application to visualize and analyze networks in soccer. The Ultimate Performance Analysis Tool (uPATO) allows observing, codifying, importing, visualizing, computing measures and exporting data from the observed games. The user may use a single application to work in the visualization and analysis of the match only considering the network that emerges from the game. In this paper it will be possible to observe the steps to visualize and import data and it will also be described the development of some network measures to characterize the centralities and general properties of unweighted and weighted graphs and digraphs. Finally, data from a real game will be used to test the network measures implemented and to show the values that can be exported and interpreted.