This repository contains code written in R to demonstrate a protein modelling approach based on Euclidean Distance Matrices (EDMs).
It contains three R scripts: cp.R, dsd.R and da.R, that model different structural rearrangements (circular permutation, domain swap dimerisation and domain atrophy, respectively) on the structure of an SH3 domain e1shgA1.pdb, downloaded from the ECOD database.
The utils.R file contains code shared by all the scripts and imports required packages.
The files ecod_domains.id and protein_bounds.tsv contain the list of 20 ECOD domain representatives and the lookup table of distance bounds extracted from them, respectively. Running times to generate C-alpha and backbone models of circular permutations (CP) and domain swap dimers (DSD) for each of the 20 ECOD domains can be found in the file runtimes_ecod.tsv.
The only requirement is R version 3.6 with the following packages that can be installed from CRAN: dplyr, bio3d, and edmcr.
If you have problems installing the edmcr package, try installing it from GitHub with devtools using:
library(devtools)
install_github("lafita/edmcr")
Scripts can be run in Rstudio or from the command line using Rscript (within this directory):
Rscript cp.R
This is a proof of concept only, so input parameters are hard-coded in the scripts for simplicity.
To use custom protein structures manually edit the input and output variables using the path to the new PDB file, and adjust the other options.
If you need help modelling large numbers of structures, please get in touch.
The R source code is released under an MIT license.
The data files are made available under a CC BY 4.0 license.
Lafita A and Bateman A. Modelling structural rearrangements in proteins using Euclidean distance matrices. F1000Research 2020, 9:728 https://doi.org/10.12688/f1000research.25235.1