Harnessing protein folding neural networks for peptide–protein docking

Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been developed for the in silico folding of protein monomers, AlphaFold2 also enables quick and accurate modeling of peptide-protein interactions. Our simple implementation of AlphaFold2 generates peptide-protein complex models without requiring multiple sequence alignment information for the peptide partner, and can handle binding-induced conformational changes of the receptor. We explore what AlphaFold2 has memorized and learned, and describe specific examples that highlight…

• EC
  European Commission

  Award: 860517 — UBIMOTIF
• US
  United States-Israel Binational Science Foundation

  Award: 207/2015
• IS
  Israel Science Foundation

  Awards: 717/2017, 301/2021