PEP-FOLD -- De Novo Peptide Structure Prediction
What you can do:
Use to predict peptide structures from amino acid sequences.
Highlights:
- PEP-FOLD is an online service aimed at de novo modelling of 3D conformations for peptides between 9 and 25 amino acids in aqueous solution.
- Using a hidden Markov model-derived structural alphabet (SA) of 27 four-residue letters, it first predicts the SA letter profiles from the amino acid sequence and then assembles the predicted fragments by a greedy procedure driven by a modified version of the OPEP coarse-grained force field.
- Starting from an amino acid sequence, PEP-FOLD performs series of 50 simulations and returns the most representative conformations identified in terms of energy and population.
- Using a benchmark of 25 peptides with 9-23 amino acids, and considering the reproducibility of the runs, PEP-FOLD locates lowest energy conformations differing by 2.6 A Calpha root mean square deviation from the full NMR structures.
Keywords:
- protein structure prediction
- tertiary structure
- protein folding
Literature & Tutorials:
This record last updated: 08-14-2009