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Documentation for the BuildPeptide utility application
Author
Barak Raveh

Metadata

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

Code and Demo

New_Library contains code for this 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.