ensECBS

Description

Scripts to run ensemble evolutionary chemical binding similarity (ensECBS).

Directory:

scripts/ - script directory for running ensECBS model.

example/ - test examples for ensECBS run.

RF_Models_Integrated/ - directory for pre-built models. Pfam, Family, Superfamily, Target-ECBS, and ensemble ensECBS models should be downloaded from https://sandbox.zenodo.org/record/297093#.XQgtfIgzaUk

Prerequisites:

Before running ensECBS script, please install the prerequisite programs and edit the path variables in the scripts.

R - tested version 3.4.2

Perl - tested version v5.16.3

R ranger package (0.8.0 or higher)

ChemmineOB package,

source("https://bioconductor.org/biocLite.R")
biocLite("ChemmineOB") 
biocLite("ChemmineR")

Script to run ensECBS

perl scripts/ensECBS_calc_script.pl

Usage: perl ensECBS_calc_script.pl -db <db.mat> -seed <seed.mat> -pair_mat <seed_db.mat> -out -overwrite -overwrite_model -overwrite_pair_mat -delete_file -help

Options:

-db : data mat file (necessary)

-seed : query mat file (necessary)

-pair_mat : paired mat file, if used, -db & -seed options will be ignored

-out : out file name (necessary)

-overwrite : re-calculate all result files

-overwrite_model : re-calcuate model score generation step

-overwrite_pair_mat : re-generate paired mat file

-delete_file : delete all intermediate files

Run examples

See ./example/TEST_example.txt file

Contributors

Keunwan Park (keunwan@kist.re.kr)