https://github.com/gersteinlab/frustration
https://github.com/gersteinlab/frustration
Last synced: 2 months ago
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- Host: GitHub
- URL: https://github.com/gersteinlab/frustration
- Owner: gersteinlab
- License: gpl-3.0
- Created: 2016-07-21T17:47:18.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2016-08-16T22:54:52.000Z (almost 9 years ago)
- Last Synced: 2025-01-20T12:07:53.852Z (4 months ago)
- Language: Python
- Size: 4.93 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](http://salilab.org/modeller/wiki/Mutate%20model)** 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