Ultra-fast in-silico structure mutation
☆36Apr 9, 2025Updated 10 months ago
Alternatives and similar repositories for EMBER3D
Users that are interested in EMBER3D are comparing it to the libraries listed below
Sorting:
- ☆11Aug 3, 2023Updated 2 years ago
- Structure-conditioned masked language modeling for protein sequence design☆71Jan 31, 2024Updated 2 years ago
- Generative diverse protein backbones by protein language model☆34Updated this week
- ☆10Apr 1, 2022Updated 3 years ago
- ☆10Feb 3, 2026Updated last month
- ☆10Nov 10, 2023Updated 2 years ago
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Oct 16, 2022Updated 3 years ago
- SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.☆21Jan 17, 2024Updated 2 years ago
- ☆110Nov 28, 2023Updated 2 years ago
- A series of scripts that facilitate the prediction of user-defined protein structural properties using AlphaFold2☆11Aug 28, 2023Updated 2 years ago
- Some scripts that I keep using over and over.☆21Jul 5, 2025Updated 7 months ago
- Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile☆72Aug 26, 2024Updated last year
- ProtT5 (Transformer) embeddings used for residue wise disorder prediction in proteins☆11Mar 11, 2024Updated last year
- Source code of the paper "Protein Sequence and Structure Co-Design with Equivariant Translation"☆24Sep 18, 2023Updated 2 years ago
- A collection of *fold* tools☆302Aug 8, 2025Updated 6 months ago
- Code for our paper "Protein sequence design with a learned potential"☆34Aug 5, 2021Updated 4 years ago
- ☆18Oct 30, 2023Updated 2 years ago
- Benchmarking Pipeline for Prediction of Protein-Protein Interactions☆14Feb 7, 2022Updated 4 years ago
- ☆43Jan 10, 2024Updated 2 years ago
- Neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis, and allostery from deep mutational sca…☆55Apr 10, 2025Updated 10 months ago
- ☆117Dec 7, 2022Updated 3 years ago
- ☆20Oct 4, 2022Updated 3 years ago
- ☆18Mar 13, 2024Updated last year
- Explore protein fold space with deep generative models☆16Aug 5, 2024Updated last year
- ☆134Jun 3, 2025Updated 9 months ago
- A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2☆98Aug 29, 2023Updated 2 years ago
- ☆82Jun 29, 2025Updated 8 months ago
- An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM☆38May 28, 2025Updated 9 months ago
- Rendering protein mutation movies from predicted 3D structures☆20Dec 7, 2023Updated 2 years ago
- Aligning protein generative models with experimental fitness☆119Oct 16, 2025Updated 4 months ago
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆38Jul 25, 2024Updated last year
- Codebase for our preprint using trRosetta to design proteins with discontinuous functional sites, found here: https://www.biorxiv.org/con…☆16Oct 27, 2021Updated 4 years ago
- Pipeline for Nanopore sequencing: demultiplexing, variant calling, and quality visualization with error handling.☆11Jan 25, 2026Updated last month
- Protein hallucination and inpainting with RoseTTAFold☆279Mar 30, 2023Updated 2 years ago
- Code for our paper "Protein sequence design with a learned potential"☆82Sep 8, 2023Updated 2 years ago
- Implementation of Protein Invariant Point Packer (PIPPack)☆35May 28, 2024Updated last year
- ☆84Nov 25, 2025Updated 3 months ago
- ☆91Sep 7, 2022Updated 3 years ago
- E(3) equivariant graph neural network for PPI site prediction☆10Sep 18, 2023Updated 2 years ago