Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)
☆268Apr 27, 2025Updated 10 months ago
Alternatives and similar repositories for ProteinWorkshop
Users that are interested in ProteinWorkshop are comparing it to the libraries listed below
Sorting:
- The official implementation of the NeurIPS'23 paper ProteinInvBench: Benchmarking Protein Design on Diverse Tasks, Models, and Metrics☆200Sep 18, 2024Updated last year
- Fast protein backbone generation with SE(3) flow matching.☆315Jul 19, 2024Updated last year
- Official repository for the ProteinGym benchmarks☆394Jan 12, 2026Updated last month
- Saprot: Protein Language Model with Structural Alphabet (AA+3Di)☆569Nov 19, 2025Updated 3 months ago
- Protein structure datasets for machine learning.☆115Apr 22, 2025Updated 10 months ago
- Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion☆59May 6, 2024Updated last year
- GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)☆317Jun 13, 2025Updated 8 months ago
- Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"☆129Nov 19, 2025Updated 3 months ago
- Versatile computational pipeline for processing protein structure data for deep learning applications.☆274Feb 14, 2024Updated 2 years ago
- Bilingual Language Model for Protein Sequence and Structure☆301Jan 2, 2025Updated last year
- ☆255Jul 31, 2024Updated last year
- Implementation for SE(3) diffusion model with application to protein backbone generation☆415Jul 3, 2023Updated 2 years ago
- Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)☆81Mar 7, 2024Updated 2 years ago
- FoldFlow: SE(3)-Stochastic Flow Matching for Protein Backbone Generation☆275Dec 10, 2024Updated last year
- Awesome Protein Representation Learning☆687Nov 16, 2024Updated last year
- Diffusion-based all-atom protein generative model.☆232Aug 27, 2025Updated 6 months ago
- Protein Graph Library☆1,163Updated this week
- ☆217Mar 2, 2024Updated 2 years ago
- EigenFold: Generative Protein Structure Prediction with Diffusion Models☆180Apr 6, 2023Updated 2 years ago
- AlphaFold Meets Flow Matching for Generating Protein Ensembles☆517Oct 21, 2025Updated 4 months ago
- A generative model for programmable protein design☆801Apr 11, 2024Updated last year
- Diffusion models of protein structure; trigonometry and attention are all you need!☆564Dec 12, 2023Updated 2 years ago
- A geometry-complete SE(3)-equivariant perceptron network (GCPNet) for 3D graphs. (Bioinformatics)☆52Apr 20, 2025Updated 10 months ago
- ☆212Sep 24, 2024Updated last year
- Compressing protein structures effectively with torsion angles☆188Feb 10, 2026Updated 3 weeks ago
- ✌🏻 Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures (NeurIPS 2022)☆354Jun 29, 2023Updated 2 years ago
- ESM-GearNet for Protein Structure Representation Learning (https://arxiv.org/abs/2303.06275)☆111Oct 23, 2023Updated 2 years ago
- Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)☆229Dec 29, 2023Updated 2 years ago
- Dataset and package for working with protein-protein interactions in 3D☆105Apr 28, 2025Updated 10 months ago
- An all-atom protein structure dataset for machine learning.☆360Mar 16, 2024Updated last year
- ☆97Oct 15, 2024Updated last year
- Inference code for PoET: A generative model of protein families as sequences-of-sequences☆93Apr 24, 2024Updated last year
- 🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2…☆82May 16, 2025Updated 9 months ago
- Structure-conditioned masked language modeling for protein sequence design☆71Jan 31, 2024Updated 2 years ago
- Plausibility checks for generated molecule poses.☆361Updated this week
- Protein Ligand INteraction Dataset and Evaluation Resource☆273Feb 21, 2026Updated 2 weeks ago
- Making Protein Design accessible to all via Google Colab!☆888Feb 27, 2026Updated last week
- Implementation of FlowSite and HarmonicFlow from the paper "Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding …☆105Jul 30, 2024Updated last year
- ☆118Dec 7, 2022Updated 3 years ago