Fragger: a protein fragment picker for structural queries [version 2; referees: 2 approved]

Fragger: a protein fragment picker for structural queries [version 2; referees: 2 approved]

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Sport Canteen 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possibly containing gaps.For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures.These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments.Fragger is a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 Medical and Ambulatory supplies / Incontinence useful for protein design, loop grafting and related structural bioinformatics tasks.