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@mnielLab Professor Morten Nielsen's Immunoinformatics and Machine Learning Lab at DTU Bioinformatics

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    22 repositories

    • BepiPocket-1.0

      Public
      Structure Prediction Tool for Antibody-Antigen Complexes
      Python
      •0•7•0•0•Updated Apr 28, 2026Apr 28, 2026

    • vaxpred-proj

      Public
      Code and data for vaxpred project
      Python
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • ImmunoGeNN

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 2026

    • NetTCR-struc

      Public
      Python
      •0•7•0•0•Updated Mar 17, 2026Mar 17, 2026

    • NetTCR-2.2

      Public
      Sequence-based prediction of peptide-TCR interactions using paired chain data
      machine-learningbioinformaticsimmunology
      machine-learningbioinformaticsimmunologyt-cell-receptorimmunoinformaticsepitopes
      Python
      •
      Other
      •6•13•1•0•Updated Feb 2, 2026Feb 2, 2026

    • gefion-containers

      Public
      Code and guides for setting up apptainer containers on Gefion HPC to run AlphaFold, Chai, BepiPocket, Boltz, Boltzgen
      Shell
      •1•0•0•0•Updated Jan 13, 2026Jan 13, 2026

    • tcrcluster_backend

      Public
      Python
      •0•1•0•0•Updated Nov 3, 2025Nov 3, 2025

    • AbEpiTope-1.0

      Public
      AbEpiTope-1.0 is a computational tool that features two scores: AbEpiScore-1.0, designed for assessing the accuracy of modelled AbAg interfaces, and AbEpiTarget…
      Python
      •5•32•1•0•Updated Oct 5, 2025Oct 5, 2025

    • AbAgIoU

      Public
      Computing the IoU metrics for evaluating the modelling accuracy of antibody-antigen complexes
      Python
      •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

    • ImmunoMSA

      Public
      Repo containing code and workflows for creating MSA inputs for structural modelling (AlphaFold, Chai1, Boltz etc.)
      Python
      •0•0•0•0•Updated May 9, 2025May 9, 2025

    • itrap

      Public
      Improved T-cell Receptor Antigen Pairing
      Python
      •0•3•0•1•Updated Mar 11, 2025Mar 11, 2025

    • esm2_utilities

      Public
      Installation guide with a little utilization code for protein language model ESM2
      Python
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • abepitope_exampledata

      Public
      Example data for AbEpiTope-1.0
      0•0•0•0•Updated Oct 12, 2024Oct 12, 2024

    • 22125_algobio_nn

      Public
      Repository for the neural networks part of (22125) Algorithms in Bioinformatics
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

    • NetTCR-IMMREP-2023

      Public
      NetTCR entries for the IMMREP 2023 kaggle competition
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

    • NetTCR-2.1

      Public
      This repo contains the code to train and test NetTCR-2.1 models
      Python
      •0•1•0•0•Updated Aug 23, 2023Aug 23, 2023

    • ITRAP_benchmark

      Public
      This repo contains the 10x Genomic datasets filtered using ATRAP and ICON denoising frameworks.
      0•1•0•0•Updated Jul 11, 2023Jul 11, 2023

    • Master_MFJ

      Public
      This repository contains the model architectures and code used for training the models in the Master thesis by Mathias Fynbo Jensen
      Python
      •0•0•0•0•Updated Mar 6, 2023Mar 6, 2023

    • train_NetTCR

      Public
      Python
      •0•1•0•0•Updated Sep 20, 2022Sep 20, 2022

    • NetTCR-2.0

      Public
      NetTCR-2.0. Sequence-based prediction of peptide-TCR binding
      Python
      •12•36•5•0•Updated Mar 29, 2022Mar 29, 2022

    • NetMHCphosPan-1.0

      Public
      TeX
      •0•2•0•0•Updated Aug 12, 2021Aug 12, 2021

    • netTCR

      Public
      predicting peptide and TCR interaction
      Python
      •
      GNU General Public License v3.0
      •5•20•4•0•Updated Jan 27, 2021Jan 27, 2021
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