This is the source code for ITCell, a method for integrative T-cell epitope prediction. See D. Schneidman-Duhovny et al. for details.
A web server is also available.
Installation
ITCell will likely only work on a Linux system.
First, download or clone this repository. Then download the prerequisites:
- IMP (the scripts expect to find the
soap_scorebinary in the PATH). - SCWRL 4 (the scripts expect the Scwrl4 executable to be found in the PATH).
- MultiProt (the scripts expect
to use
scripts/multiprot.Linuxand were developed with version 1.93).
Next, download the support libraries, libs.tar.xz, from
https://salilab.org/itcell-lib/
or 10.5281/zenodo.3226992
and extract into the libs directory.
Usage
Run scripts/runITCell.pl giving it the MHC type, the path to a TCR PDB
file, and the path to a file containing the antigen sequence, e.g.
perl <repo>/scripts/runITCell.pl DRB1*0101 TCR.pdb antigen_seq.txt
License
ITCell is Copyright 2018 Dina Schneidman-Duhovny, and is available under the
terms of the GNU Lesser GPL; see file LICENSE.