PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex

Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54. doi: 10.1093/nar/gkw329. Epub 2016 Apr 29.


Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3Å from the experimental conformation and return a native-like pose in the first 10 clusters for 52% of the targets. PEP-FOLD3 is available at

MeSH terms

  • Algorithms
  • Amino Acids / chemistry
  • Benchmarking
  • Internet
  • Models, Molecular
  • Peptides / chemistry*
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Software*
  • Solutions


  • Amino Acids
  • Peptides
  • Proteins
  • Solutions