Repositories list

• NaturalPPLuM

  Public
  Repository of the paper "Exploring sequence landscape of biosynthetic gene clusters with protein language models" published at ICML2024 workshop Machine Learnin…

  deep-learningtransfer-learningbiosynthetic-gene-clusters+ 4

  deep-learningtransfer-learningbiosynthetic-gene-clusterssmall-dataicml-2024esm2ml4lms

  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Apr 25, 2026Apr 25, 2026

• DataSAIL

  Public
  DataSAIL is a tool to split datasets while reducing information leakage.

  machine-learningoptimizationilp+ 3

  machine-learningoptimizationilpscipdataset-splitilp-problem

  Python

  •

  MIT License

  •44 forks•5151 stars•66 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• LoReMINE

  Public
  Long Read-based Microbial genome mining pipeline

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• ALPAR

  Public
  Single Reference Antimicrobial Resistance

  machine-learningamrsingle-reference-amr

  machine-learningamrsingle-reference-amr

  Python

  •

  MIT License

  •00 forks•77 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• SMTB2024

  Public
  Python

  •11 fork•11 star•11 issue•22 pull requests•Updated Apr 20, 2026Apr 20, 2026

• structguy

  Public
  Python

  •

  GNU Lesser General Public License v2.1

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• StructMAn

  Public
  Python

  •

  GNU Lesser General Public License v2.1

  •11 fork•33 stars•00 issues•00 pull requests•Updated Mar 24, 2026Mar 24, 2026

• epistasis_proteingym

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• Lasso_project

  Public
  CSS

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 13, 2026Mar 13, 2026

• ESP_Leak_Analysis

  Public
  Addressing data leakage in a deep-learning model for predicting small molecule substrates of enzymes

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Feb 26, 2026Feb 26, 2026

• LigandXai

  Public
  Jupyter Notebook

  •22 forks•22 stars•00 issues•00 pull requests•Updated Feb 19, 2026Feb 19, 2026

• rindti

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 23, 2026Jan 23, 2026

• PLMBench

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 19, 2025Dec 19, 2025

• StructGuy_evaluation

  Public
  Python

  •

  GNU Lesser General Public License v2.1

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 29, 2025Nov 29, 2025

• EMMA

  Public
  EMMA: A General Transformer-Based Multi-Task Learning Framework for Enzyme–Small Molecule Interaction Prediction

  Jupyter Notebook

  •00 forks•33 stars•00 issues•00 pull requests•Updated Nov 5, 2025Nov 5, 2025

• GlyLES

  Public
  A tool to convert IUPAC representations of glycans into SMILES strings.

  antlr4smilesgrammar-parser+ 2

  antlr4smilesgrammar-parserglycansiupac

  Python

  •

  MIT License

  •77 forks•1616 stars•22 issues•00 pull requests•Updated Aug 19, 2025Aug 19, 2025

• gfp_project

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 5, 2025Aug 5, 2025

• SMTB2025_PLM

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 14, 2025Jul 14, 2025

• SMTB2025_AMR

  Public
  SMTB 2025 Repository

  Python

  •66 forks•33 stars•00 issues•11 pull request•Updated Jul 13, 2025Jul 13, 2025

• useful_scripts

  Public
  A repository to share our useful scripts in, between our group and others

  Jupyter Notebook

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 21, 2025Mar 21, 2025

• EpiPAMPAS

  Public
  Rapid detection of intra-protein epistasis via parsimonious ancestral state reconstruction and counting parallel mutations

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 18, 2024Dec 18, 2024

• ProtPreTrain

  Public
  Protein structure pretraining

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 4, 2024Nov 4, 2024

• LP-PDBBind

  Public
  Jupyter Notebook

  •77 forks•00 stars•00 issues•00 pull requests•Updated Feb 1, 2024Feb 1, 2024

• GraphPLI

  Public
  Structure-informed Prediction of Interactions of Lectins and Glycans

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 27, 2023Nov 27, 2023

• alphafold_non_docker

  Public
  AlphaFold2 non-docker setup

  Shell

  •126126 forks•378378 stars•2222 issues•22 pull requests•Updated Nov 24, 2023Nov 24, 2023

• SMTB_2023

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 23, 2023Aug 23, 2023

• CompressBinaryTable

  Public
  Compresses binary tables

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 2, 2023Jun 2, 2023

• datasail_tape

  Public
  Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology…

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •135135 forks•00 stars•00 issues•00 pull requests•Updated Mar 24, 2023Mar 24, 2023

• scala

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 6, 2023Feb 6, 2023

• panpa

  Public
  PanPA is a tool for generating alignment of protein graphs

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 21, 2022Nov 21, 2022