Metadata

Author: Barak Raveh

Last updated July 24, 2011 ; PI: Ora Schueler-Furman (oraf@ekmd.huji.ac.il).

Code and Demo

Application source code: rosetta/main/source/src/apps/public/flexpep_docking/BuildPeptide.cc
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.

Options

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

Tips

 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.

The BuildPeptide utility application