Author: Barak Raveh

Last updated July 24, 2011 ; PI: Ora Schueler-Furman (

Code and Demo

  • Application source code: rosetta/main/source/src/apps/public/flexpep_docking/
  • For a demonstration of a basic run of the BuildPeptide utility application, see rosetta/main/tests/integration/tests/BuildPeptide

Application purpose

Building an extended peptide or protein structure from a FASTA file (to help preparing input for peptide docking protocol, etc.).

Input Files

BuildPeptide requires a fasta file in standard format as input.


Flag Description Type
-in:file:fasta FASTA file with peptide sequence string
-out:file:o output PDB file name string
-helix (optional) Make a helical, rather than extended, peptide bool
-phi (advanced) Specify the phi backbone angle to repeat, default -135.0 real
-psi (advanced) Specify the psi backbone angle to repeat, default 135.0 real


 BuildPeptide.{ext} -database ${mini_db} -in:file:fasta input.fasta -out:file:o peptide.pdb

Expected Outputs

The output of a BuildPeptide run is a PDB-format file of the peptide in an extended full-atom conformation. Side-chain rotamers are arbitrary. This can be used for e.g., creating an initial structure for a FlexPepDock ab-initio run.

See Also