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Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection

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Academic year: 2021

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Figure

Figure 1: Example of an alignment graph used here to compare the structures of two proteins
Figure 2: Example of symmetry issues. Even though, vertex v l = ( L, L 0 ) belongs to the extension of seed ( v i , v j , v k ), points L and L 0 lie on different sides of the plane defined by optimally superimposed triangles IJ K and I 0 J 0 K 0 .
Figure 3: Illustration of the guarantee on the similarity of internal distances between two pairs of atoms v l = ( L, L 0 ) and v m = ( M, M 0 ), here represented in yellow, added to a seed ( v i , v j , v k ) represented in blue
Figure 4 shows an overview of our parallel implementation. Multiple seeds are treated simultaneously to form a coarse-grain level of parallelism, while a finer grain parallelism is used when extending a single seed.
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