Fragger

Protein modeling and design activities often require querying the Protein Data
Bank (PDB) with a structural fragment, possibly containing gaps. For some
applications, it is preferable to work on a specific subset of the PDB or with
unpublished structures. These requirements, along with specific user needs,
motivated the creation of a new software to manage and query 3D protein
fragments. Fragger is a protein fragment picker that allows protein fragment
databases to be created and queried. All fragment lengths are supported and any
set of PDB files can be used to create a database. Fragger can efficiently search
a fragment database with a query fragment and a distance threshold. Matching
fragments are ranked by distance to the query. The query fragment can have
structural gaps and the allowed amino acid sequences matching a query can be
constrained via a regular expression of one-letter amino acid codes. Fragger also
incorporates a tool to compute the backbone RMSD of one versus many fragments in
high throughput. Fragger should be useful for protein design, loop grafting and
related structural bioinformatics tasks.

Fragger: a protein fragment picker for structural queries.

Fragger is a software tool for creating and searching protein fragment databases. The Fragger algorithm computes the root-mean-square deviation (RMSD) and uses the RMSD distance threshold to rank and query the fragments.

Fragger

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