Peptiderive server: derive peptide inhibitors from protein-protein interactions

Nucleic Acids Res. 2016 Jul 8;44(W1):W536-41. doi: 10.1093/nar/gkw385. Epub 2016 May 3.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Cyclization
  • Disulfides / chemistry
  • Internet*
  • Oncogene Proteins, Viral / antagonists & inhibitors
  • Oncogene Proteins, Viral / chemistry
  • Oncogene Proteins, Viral / pharmacology
  • Peptides / chemistry*
  • Peptides / pharmacology*
  • Protein Binding / drug effects
  • Protein Interaction Maps*
  • Proteins / antagonists & inhibitors*
  • Proteins / chemistry*
  • Software*
  • Time Factors
  • User-Computer Interface

Substances

  • Disulfides
  • Oncogene Proteins, Viral
  • Peptides
  • Proteins
  • oncogene protein E1, Human papillomavirus type 18
  • oncogene protein E2, Human papillomavirus type 18