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.
authors.affiliation: Department of Microbiology and Molecular Genetics, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel Department of Chemical and Biomolecular Engineering, John Hopkins University, Baltimore, MD 21218, USA.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Sedan
authors.affiliation: Department of Microbiology and Molecular Genetics, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel.
authors.forename: Orly
authors.initials: O
authors.lastname: Marcu
authors.affiliation: Racah Institute of Physics, Hebrew University of Jerusalem, Israel.
authors.forename: Sergey
authors.initials: S
authors.lastname: Lyskov
authors.affiliation: Department of Microbiology and Molecular Genetics, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel oraf@ekmd.huji.ac.il.
authors.forename: Ora
authors.initials: O
authors.lastname: Schueler-Furman
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003500:Cyclization; D004220:Disulfides / Q000737:chemistry; D020407:Internet; D009856:Oncogene Proteins, Viral / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000494:pharmacology; D010455:Peptides / Q000737:chemistry* / Q000494:pharmacology*; D011485:Protein Binding / Q000187:drug effects; D060066:Protein Interaction Maps; D011506:Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry*; D012984:Software; D013997:Time Factors; D014584:User-Computer Interface
chemical_list: D004220:Disulfides; D009856:Oncogene Proteins, Viral; D010455:Peptides; D011506:Proteins; C084762:oncogene protein E1, Human papillomavirus type 18; C069102:oncogene protein E2, Human papillomavirus type 18