Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

By Nir London, Barak Raveh, Eyal Cohen, Guy Fathi, O. Schueler‐Furman. Nucleic Acids Res., 2011

396 citations recorded by the source corpus.

Peptide–protein interactions are among the most prevalent and important interactions in the cell, but a large fraction of those interactions lack detailed structural characterization. The Rosetta FlexPepDock web server (http://flexpepdock.furmanlab.cs.huji.ac.il/) provides an interface to a high-resolution peptide docking (refinement) protocol for the modeling of peptide–protein complexes, implemented within the Rosetta framework. Given a protein receptor structure and an approximate, possibly inaccurate model of the peptide within the receptor binding site, the FlexPepDock server refines the peptide to high resolution, allowing full flexibility to the peptide backbone and to all side chains. This protocol was extensively tested and benchmarked on a wide array of non-redundant peptide–protein complexes, and was proven effective when applied to peptide starting conformations within 5.5 Å backbone root mean square deviation from the native conformation. FlexPepDock has been applied to several systems that are mediated and regulated by peptide–protein interactions. This easy to use and general web server interface allows non-expert users to accurately model their specific peptide–protein interaction of interest.

Subfields: Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/d143d121af1c3ab904a247b2f9642a6938eb3825

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Citations in the corpus

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site (2015, neutral): “The promising CABS-dock extensions include: for example, adding a refinement step (19,23); incorporation of experimental data; increasing the flexibility of appropriate receptor fragments (e.”
A Comprehensive Review on Current Advances in Peptide Drug Development and Design (2019, methodology): “Rosetta FlexPepDock is a Monte Carlo-based method that minimizes optimization steps to yield high-quality conformational sampling for well-characterized binding motifs with hotspot residues [93,94].”
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex (2016, methodology): “The RosettaFlexPepDock (19) server will refine the structure of a peptide bound to a receptor, Galaxypepdock (20) performs similarity based docking using existing templates and the CABS-dock server (21) performs a blind docking which can be time consuming.”
New additions to the ClusPro server motivated by CAPRI (2017, methodology): “…much poorer.13 However, in 2012 we have introduced a special DARS-type potential for this type of interactions, which provided some improvement.16 The last CAPRI evaluation meeting in April 2016 focused on the results of rounds 28–29 and 31–35 that included targets 59–67 and 95–105, respectively.”
A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking (2013, neutral): “FlexPepDock, which is also available as a webserver, assumes knowledge of the binding site (anchor residues) to build and refine the peptide onto its receptor [24].”
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides (2012, background): “Recent efforts from the community of computer scientists have tackled various aspects including the design of generic databases devoted to peptide–protein interactions such as PepX (8), the problem of protein–peptide docking (9), the search for peptidomimetics (10) and the development of fast peptid”