Visualisations of data are at the core of every publication of scientific research results. They have to be as clear as possible to facilitate the communication of research. As data can have differ…

AlphaFold 3 inference pipeline.

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

OpenChord is a Python library for creating chord diagrams.

Inference of TCR motifs

A new markup-based typesetting system that is powerful and easy to learn.

Convert Obsidian vaults to collection of notes readable by Cosma and Zettlr

An exploration of apo vs holo peptide:MHC:TCR structures

Working with molecular structures in pandas DataFrames

Foldseek enables fast and sensitive comparisons of large structure sets.

Using TCR and expression for sequence embedding

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

Tool for rapid clustering of antibody models by the structure of their CDRs.

flexible CDR based distance metrics

TCR2vec is a deep representation learning framework of T-cell receptor sequence and function

Template for compiling slides in latex

checkcites is a Lua script written for the sole purpose of detecting undefined/unused references from LaTeX auxiliary or bibliography files.

Altered TCR Ligand Affinities and Structures

Convert Machine Learning Code Between Frameworks

Matplotlib styles for scientific plotting

The Slurm (or Simple) Profiling Service is a lightweight job profiler which bridges the gap between numerical job stats and full-blown application profiling

Predict the structure of immune receptor proteins

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.

PyTorch implementation of bimodal neural networks for drug-cell (pharmarcogenomics) and drug-protein (proteochemometrics) interaction prediction

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2