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_score binary 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.Linux and 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.