FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

ABSTRACT: Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of

SUBMITTER: Budowski-Tal I 

PROVIDER: S-EPMC2840415 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature