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Modeling and Design of Peptidomimetics to Modulate Protein–Protein Interactions

  • Andrew M. Watkins
  • Richard Bonneau
  • Paramjit S. AroraEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1561)

Abstract

We describe a modular approach to identify and inhibit protein–protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.

Key words

Peptidomimetics Protein–protein interactions Inhibitor design Computational design 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Andrew M. Watkins
    • 1
  • Richard Bonneau
    • 2
    • 3
  • Paramjit S. Arora
    • 4
    Email author
  1. 1.Department of ChemistryNew York UniversityNew YorkUSA
  2. 2.Department of Biology, Center for Genomics and Systems BiologyNew York UniversityNew YorkUSA
  3. 3.Computer Science Department, Courant Institute of Mathematical SciencesNew York UniversityNew YorkUSA
  4. 4.Department of ChemistryNew York UniversityNew YorkUSA

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