/Frustration

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

Frustration Project

This repository contains source code for workflow evaluating the change in Localized frustration index of a protein residue upon mutation. The input to this workflow is VAT output file, which is ran on the user provided list of single nucleotide variants(SNVs). More details about running VAT can be found here (http://vat.gersteinlab.org/).

Dependencies

In order to calculate frustration changes, one need to Install following set of tools

  1. VAT (http://vat.gersteinlab.org/)

  2. BlastP

  3. Modeller

  4. mutate_model.py script from the Modeller in your working directory

  5. pdbTools (https://github.com/harmslab/pdbtools)

  6. Frustration code

  7. BALL (http://www.ball-project.org/Downloads)

8)Contrib (http://www.ball-project.org/Downloads/index_html/Contrib/)

Workflow

This workflow consist of three steps for evaluating changes in frustration:

1) Parsing VAT output of all SNVs to etxract residue position and residue identity for the mutated residue on protein sequence

Usage:

parseVatOut.py -d dataResourceFile -v vatOutputFile -b bioMartFile -type snpType

parseVatOut.py (-h | --help)

dataResourceFile = gencode v19 translated fasta sequence

bioMartFile = Biomart output file containing GeneId,TranscriptId and PdbId (genocde v19)

snpType = nonsynonymous

2) Mapping each SNV onto user-provided list of PDB strcuture ange generating mutated PDB

Usage:

mapSNP2PDB.py -p pdbIdList -b bioMartFile -I snpSummaryFile -B blastPDir -M modellerDir -P pbdSeqDir -O outLogFile

mapSNP2PDB.py (-h | --help)

pdbIdList = list of high resolution PDBs for mapping SNPs

bioMartFile = Biomart output file containing GeneId,TranscriptId and PdbId (genocde v19)

snpSummaryFile = generated by parseVatOut.py in the previous step

blastPDir = BlastP directory

modellerDir = Modeller directory

pdbSeqDir = pdbTool directory

3) Evaluating Frustration changes of residues

Usage:

extractFrustrationInfo.py -I mappedSNPInfo -nd nativePDBDir -md mutPDBDir -F frstnExecDir -P pdbSeqDir -O frustrationOutFile

extractFrustrationInfo.py (-h | --help)

mappedSNPInfo = mapped SNV info file generated by mapSNP2PDB.py

nativePDBDir = Directory where you store your native PDBs

mutPDBDir = Driectory where you store your mutated/modeled PDBs

frstnExecDir = Frustration executable location

pdbSeqDir = pdbTool directory