Top Five Metal Coordination Geometry Scripts

This set of scripts runs the full set of analyses used in:

Yao S, Flight RM, Rouchka EC, Moseley HN. (2017) “Aberrant coordination geometries discovered in the most abundant metalloproteins.” Proteins: Structure, Function, and Bioinformatics, 85(5): 885-907

If you use these scripts, please cite the above paper.

Citation and Licensing

Please see the individual packages for their license information, and the mainScripts/README.md and LICENSE for citing and license information of the metalloprotein analysis scripts.

Installation

This repository contains the main scripts for the analysis pipeline. For the whole package that can fully regenerate the data for the paper, including dependant packages, download the tarballed files at:

https://figshare.com/articles/Five_metal_manuscript/4229297

You can un-tar the downloaded file:

tar -xzpf fiveMetalManuscript.tar.gz

This creates the directory fiveMetalManuscript, that contains a set of directories:

• atom2seq: R package that does alignment and functional enrichment
• categoryCompare2: allows arbitrary enrichment calculations
• mainScripts: the main scripts that do the analysis
• output_metal_org: the original outputs generated for each and combined metal
• metalPDB: supporting scripts in generating metalloprotein PDB list

Prerequisites

To run it, you will need 32GB of Ram, and also need to install (on Linux):

perl::Math::MatrixReal
perl::Clone
perl::Thread::Queue
perl::JSON (optional for certain settings)
perl::Data::Dumper::Concise (optional for certain settings)

Interproscan (https://code.google.com/p/interproscan/)

libxml2-devel (for compiling some R packages from source)

R
R-devel

And then the following R packages:

Biostrings
Biobase
AnnotationDbi
Category
GO.db
annotate
clue
cluster
randomForest
ggplot2
gridExtra

In addition, a custom package also need to be installed, which are included. To install those, the easiest method is using devtools:

R
setwd("atom2seq")
devtools::install()

setwd("../categoryCompare2")
devtools::install()

PDB download

You also need a local copy of the PDB.

rsync -rlpt -v -z --delete --port=33444 \ > rsync.wwpdb.org::ftp_data/structures/divided/pdb/ ./pdb

Running analysis

Counting metal sites

Use below under the mainScripts directory to reproduce the full analysis.

./run.countMetal.bh

Main analysis

Finally, for actually running the scripts, you need to modify the alias for interpro and environment variables output_dir at the top of mainScripts/run.fullanalysis.bh. Use below under the mainScripts directory to reproduce the full analysis.

./run.fullanalysis.bh

4-ligand Zn simulation

Use ./run.simulation.bh under the mainScripts directory to reproduce the full analysis.

Functional enrichmentment

Use ./run_enrichments.R under the mainScripts directory to generate the enrichment results. The easiest way to run this is by:

cd mainScripts
R
source("run_enrichments.R")

The directories that are used may need to be changed.

For manuscript figures

Run each R code in R console in the supportingScripts directory. Change input directory accordingly.

Manuscript data

The original intermediate and final results generated for each and combined metal are in corresponding output_*_org directories.

Enjoy!