Documentation for the BuildPeptide utility application

Author:

Barak Raveh

Metadata

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

Code and Demo

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

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.