Peptiderive server: derive peptide inhibitors from protein-protein interactions

Yuval Sedan; Orly Marcu; Sergey Lyskov; Ora Schueler-Furman

doi:10.1093/NAR/GKW385

Peptiderive server: derive peptide inhibitors from protein-protein interactions

Yuval Sedan, Orly Marcu, Sergey Lyskov, Ora Schueler-Furman^*

^*Corresponding author for this work

Department of Microbiology and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

64 Scopus citations

Abstract

The Rosetta Peptiderive protocol identifies, in a given structure of a protein-protein interaction, the linear polypeptide segment suggested to contribute most to binding energy. Interactions that feature a 'hot segment', a linear peptide with significant binding energy compared to that of the complex, may be amenable for inhibition and the peptide sequence and structure derived from the interaction provide a starting point for rational drug design. Here we present a web server for Peptiderive, which is incorporated within the ROSIE web interface for Rosetta protocols. A new feature of the protocol also evaluates whether derived peptides are good candidates for cyclization. Fast computation times and clear visualization allow users to quickly assess the interaction of interest. The Peptiderive server is available for free use at http://rosie.rosettacommons.org/peptiderive.

Original language	American English
Pages (from-to)	W536-W541
Journal	Nucleic Acids Research
Volume	44
Issue number	1
DOIs	https://doi.org/10.1093/NAR/GKW385
State	Published - 1 Aug 2016

Bibliographical note

Funding Information:
European Research Council under the ERC Grant Agreement [310873]; USA-Israel Binational Science Foundation [2009418]; Israel Science Foundation, founded by the Israel Academy of Science and Humanities [319/11]; The ROSIE platform is supported by NIH [R01-GM073151]. Funding for open access charge: European Research Council [310873]. Conflict of interest statement. None declared.

Publisher Copyright:
© The Author(s) 2016.

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10.1093/NAR/GKW385

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title = "Peptiderive server: derive peptide inhibitors from protein-protein interactions",

abstract = "The Rosetta Peptiderive protocol identifies, in a given structure of a protein-protein interaction, the linear polypeptide segment suggested to contribute most to binding energy. Interactions that feature a 'hot segment', a linear peptide with significant binding energy compared to that of the complex, may be amenable for inhibition and the peptide sequence and structure derived from the interaction provide a starting point for rational drug design. Here we present a web server for Peptiderive, which is incorporated within the ROSIE web interface for Rosetta protocols. A new feature of the protocol also evaluates whether derived peptides are good candidates for cyclization. Fast computation times and clear visualization allow users to quickly assess the interaction of interest. The Peptiderive server is available for free use at http://rosie.rosettacommons.org/peptiderive.",

author = "Yuval Sedan and Orly Marcu and Sergey Lyskov and Ora Schueler-Furman",

note = "Funding Information: European Research Council under the ERC Grant Agreement [310873]; USA-Israel Binational Science Foundation [2009418]; Israel Science Foundation, founded by the Israel Academy of Science and Humanities [319/11]; The ROSIE platform is supported by NIH [R01-GM073151]. Funding for open access charge: European Research Council [310873]. Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} The Author(s) 2016.",

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Peptiderive server: derive peptide inhibitors from protein-protein interactions

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