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Frag'r'Us : knowledge-based sampling of protein backbone conformations for de novo structure-based protein design
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Bonet, Jaume, Segura, Joan, Planas-Iglesias, Joan, Oliva, Baldomero and Fernandez-Fuentes, Narcis (2014) Frag'r'Us : knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. Bioinformatics, 30 (13). pp. 1935-1936. doi:10.1093/bioinformatics/btu129 ISSN 1367-4803.
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Official URL: http://dx.doi.org/10.1093/bioinformatics/btu129
Abstract
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.
Item Type: | Journal Article | ||||
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Journal or Publication Title: | Bioinformatics | ||||
Publisher: | Oxford University Press | ||||
ISSN: | 1367-4803 | ||||
Official Date: | 2014 | ||||
Dates: |
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Volume: | 30 | ||||
Number: | 13 | ||||
Page Range: | pp. 1935-1936 | ||||
DOI: | 10.1093/bioinformatics/btu129 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access |
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