Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development

We find recurring amino-acid residue packing patterns, or spatial motifs, that are characteristic of protein structural families, by applying a novel frequent subgraph mining algorithm to graph representations of protein three-dimensional structure. Graph nodes represent amino acids, and edges

structures are represented by robust graphs, and the Fast Frequent Subgraph Mining algorithm is applied to protein families to generate sets of family-specific packing motifs, i.e. amino acid residue packing patterns shared by most family members but infrequent in other proteins. The function of a protein

The SWISS-PROT protein knowledgebase

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while

ation, and termination phases of protein synthesis. Because the structures of several DNA and RNA polymerases have been determined at atomic resolution, the mechanisms of DNA and RNA synthesis are both well understood. Determination of the structure of the ribosome, however, has proven a daunting

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices

Diploid cells of budding yeast produce haploid cells through the developmental program of sporulation, which consists of meiosis and spore morphogenesis. DNA microarrays containing nearly every yeast gene were used to assay changes in gene expression during sporulation. At least seven distinct

that it outperforms the original method. Furthermore, we observe that the ranking of the descriptors is mostly independent of the interest region detector and that the SIFT based descriptors perform best. Moments and steerable filters show the best performance among the low dimensional descriptors.

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