Frag’r’Us: Knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

Jaume Bonet, Joan Segura, Joan Planas-Iglesias, Baldo Oliva, Narcis Fernandez-Fuentes

Research output: Contribution to journalArticlepeer-review

13 Citations (SciVal)
158 Downloads (Pure)

Abstract

Motivation The remodeling of short fragment(s) of the protein backbone to accommodate new function(s), fine-tune binding specificities or change/create novel protein interactions is a common task in structure-based computational design. Alternative backbone conformations can be generated de novo or by redeploying existing fragments extracted from protein structures i.e. knowledge-based. We present Frag’r’Us, a web server designed to sample alternative protein backbone conformations in loop regions. The method relies on a database of super secondary structural motifs called smotifs. Thus, sampling of conformations reflects structurally feasible fragments compiled from existing protein structures.

Availability and implementation Frag’r’Us has been implemented as web application and is available at http://www.bioinsilico.org/FRAGRUS
Original languageEnglish
Pages (from-to)1935-1936
JournalBioinformatics
Volume30
Issue number13
DOIs
Publication statusPublished - 01 Jul 2014

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