itcell-lib

Integrative T-cell epitope prediction

https://github.com/salilab/itcell-lib

Science Score: 67.0%

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 8 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary

Keywords

integrative-modeling prediction

Last synced: 10 months ago · JSON representation ·

Repository

Integrative T-cell epitope prediction

Basic Info

Host: GitHub
Owner: salilab
License: lgpl-2.1
Language: Perl
Default Branch: main
Size: 4.59 MB

Statistics

Stars: 1
Watchers: 20
Forks: 0
Open Issues: 0
Releases: 1

Topics

integrative-modeling prediction

Created about 7 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

README.md

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

Owner

Name: Sali Lab
Login: salilab
Kind: organization
Location: San Francisco, CA

Website: https://salilab.org
Twitter: salilab_ucsf
Repositories: 76
Profile: https://github.com/salilab

Laboratory of Andrej Sali at the University of California San Francisco

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Schneidman-Duhovny"
  given-names: "Dina"
- family-names: "Khuri"
  given-names: "Natalia"
- family-names: "Dong"
  given-names: "Guang Qiang"
- family-names: "Winter"
  given-names: "Michael B."
- family-names: "Shifrut"
  given-names: "Eric"
- family-names: "Friedman"
  given-names: "Nir"
- family-names: "Craik"
  given-names: "Charles S."
- family-names: "Pratt"
  given-names: "Kathleen P."
- family-names: "Paz"
  given-names: "Pedro"
- family-names: "Aswad"
  given-names: "Fred"
- family-names: "Sali"
  given-names: "Andrej"
title: "ITCell"
url: "https://github.com/salilab/itcell-lib"
preferred-citation:
  type: article
  authors:
  - family-names: "Schneidman-Duhovny"
    given-names: "Dina"
  - family-names: "Khuri"
    given-names: "Natalia"
  - family-names: "Dong"
    given-names: "Guang Qiang"
  - family-names: "Winter"
    given-names: "Michael B."
  - family-names: "Shifrut"
    given-names: "Eric"
  - family-names: "Friedman"
    given-names: "Nir"
  - family-names: "Craik"
    given-names: "Charles S."
  - family-names: "Pratt"
    given-names: "Kathleen P."
  - family-names: "Paz"
    given-names: "Pedro"
  - family-names: "Aswad"
    given-names: "Fred"
  - family-names: "Sali"
    given-names: "Andrej"
  doi: "10.1371/journal.pone.0206654"
  journal: "PLoS ONE"
  month: 11
  start: "e0206654"
  title: "Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition"
  volume: 13
  issue: 11
  year: 2018

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