softnanolab / bagelView external linksLinks
Protein Engineering via Exploration of an Energy Landscape
☆103Feb 4, 2026Updated last week
Alternatives and similar repositories for bagel
Users that are interested in bagel are comparing it to the libraries listed below
Sorting:
- Protein prediction models implemented with Modal☆30Jan 25, 2026Updated 2 weeks ago
- All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins☆120May 27, 2025Updated 8 months ago
- Sidechain conditioning and modeling for full-atom protein sequence design☆133Nov 11, 2025Updated 3 months ago
- Fold Conditioned protein design pipeline based on AF2Multimer Hallucination☆49Dec 2, 2025Updated 2 months ago
- Official repository for discrete Walk-Jump Sampling (dWJS)☆55Dec 17, 2023Updated 2 years ago
- A standardized protein design benchmark for motif-scaffolding problems☆73Jan 27, 2026Updated 2 weeks ago
- MaSIF-neosurf: surface-based protein design for ternary complexes.☆167Feb 6, 2026Updated last week
- ProteusAI is a library for the machine learning driven engineering of proteins. The library enables workflows from protein structure pred…☆76Sep 11, 2025Updated 5 months ago
- ☆22Dec 11, 2024Updated last year
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆126Sep 3, 2025Updated 5 months ago
- Learning Universal Representations of Intermolecular Interactions with ATOMICA☆199Sep 14, 2025Updated 4 months ago
- PLM-interact: extending protein language models to predict protein-protein interactions.☆60Aug 29, 2025Updated 5 months ago
- Source code for RNA-FrameFlow: SE(3) Flow Matching for 3D RNA Backbone Design☆92Oct 15, 2025Updated 3 months ago
- ☆86Dec 15, 2025Updated last month
- Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and rel…☆234Jul 24, 2025Updated 6 months ago
- composite-objective protein design☆243Feb 6, 2026Updated last week
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- A thin wrapper around ProteinMPNN for convenient sampling without having to write out or consume files☆12Apr 29, 2024Updated last year
- ☆55Jul 22, 2025Updated 6 months ago
- Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation☆146Jan 31, 2026Updated last week
- bioinformatics tools running on modal☆137Updated this week
- Making folding experiments more accessible .☆92Jul 17, 2025Updated 6 months ago
- Antibody structure prediction☆34Dec 16, 2025Updated last month
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆30Jan 23, 2026Updated 3 weeks ago
- Code for designing biased protein states☆59Nov 20, 2025Updated 2 months ago
- Code for the paper "Learning to engineer protein flexibility".☆22Jan 21, 2026Updated 3 weeks ago
- Directed evolution of proteins in sequence space with gradients☆94Oct 18, 2025Updated 3 months ago
- ☆37Aug 28, 2023Updated 2 years ago
- ☆74Mar 19, 2025Updated 10 months ago
- Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3☆198Jan 3, 2026Updated last month
- PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.☆222Nov 5, 2025Updated 3 months ago
- Geometric Algebra Flow Matching (GAFL) for Protein Backbone Generation☆17Oct 31, 2025Updated 3 months ago
- User friendly and accurate binder design pipeline☆1,007Feb 5, 2026Updated last week
- Template-based protein design with Raygun☆77Updated this week
- Predicting mutational effects on protein binding from folding energy. ICML 2025.☆40Aug 4, 2025Updated 6 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆60Jan 30, 2026Updated 2 weeks ago
- ☆27Jun 16, 2025Updated 7 months ago
- ☆25Oct 8, 2024Updated last year
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 9 months ago