The BuildPeptide utility application
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/rosetta_source/src/apps/public/flexpep_docking/BuildPeptide.cc - For a demonstration of a basic run of the BuildPeptide utility application, see
rosetta/rosetta_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 |
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.