title: Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design.
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.
authors.affiliation: Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK.
authors.forename: Jaume
authors.initials: J
authors.lastname: Bonet
authors.affiliation: Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK.
authors.forename: Joan
authors.initials: J
authors.lastname: Segura
authors.affiliation: Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK.
authors.forename: Joan
authors.initials: J
authors.lastname: Planas-Iglesias
authors.affiliation: Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK.
authors.forename: Baldomero
authors.initials: B
authors.lastname: Oliva
authors.affiliation: Structural Bioinformatics Lab (GRIB), Universitat Pompeu Fabra, Barcelona, Catalonia 08003, Spain, Department of Structure of Macromolecules, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain and Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth, SY23 3DA Ceredigion, UK.
authors.forename: Narcis
authors.initials: N
authors.lastname: Fernandez-Fuentes
mesh_terms: D051188:Knowledge Bases; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins