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Integrative T-cell epitope prediction
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README.md

README.md

DOI

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 (extract SCWRL into the scripts/scwlr4 subdirectory of this repository; the scripts expect the SCWRL executable to be found as scripts/scwrl4/Scwrl4).
  • 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.

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