The Parasol Protocol for computational mutagenesis

Protein Eng Des Sel. 2016 Jul;29(7):253-61. doi: 10.1093/protein/gzw009. Epub 2016 May 4.


To aid in the discovery and development of peptides and proteins as therapeutic agents, a virtual screen can be used to predict trends and direct workflow. We have developed the Parasol Protocol, a dynamic method implemented using the AMBER MD package, for computational site-directed mutagenesis. This tool can mutate between any pair of amino acids in a computationally expedient, automated manner. To demonstrate the potential of this methodology, we have employed the protocol to investigate a test case involving stapled peptides, and have demonstrated good agreement with experiment.

Keywords: in silico mutation; molecular dynamics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Computer Simulation
  • Humans
  • Models, Molecular
  • Mutagenesis, Site-Directed*
  • Mutation
  • Peptides / chemistry
  • Peptides / genetics
  • Proteins / chemistry*
  • Proteins / genetics*
  • Software*
  • Workflow


  • Peptides
  • Proteins