Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
☆63Oct 28, 2025Updated 4 months ago
Alternatives and similar repositories for timed-design
Users that are interested in timed-design are comparing it to the libraries listed below
Sorting:
- ☆18Mar 13, 2024Updated last year
- Structure-conditioned masked language modeling for protein sequence design☆71Jan 31, 2024Updated 2 years ago
- DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.☆30Mar 4, 2025Updated last year
- Implementation of Protein Invariant Point Packer (PIPPack)☆35May 28, 2024Updated last year
- This repository contains code for the paper: "Tertiary motifs as building blocks for the design of protein-binding peptides"☆21Jan 15, 2024Updated 2 years ago
- Design data and process for the AdaptyvBio protein design competition☆10Dec 11, 2024Updated last year
- Code for our paper "Protein sequence design with a learned potential"☆82Sep 8, 2023Updated 2 years ago
- ☆47Sep 16, 2024Updated last year
- Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protei…☆48Nov 4, 2025Updated 4 months ago
- ☆15Sep 29, 2025Updated 5 months ago
- Fast protein structure searching or your money back☆118Jan 14, 2026Updated last month
- Code for our paper "Protein sequence design with a learned potential"☆34Aug 5, 2021Updated 4 years ago
- A compilation of deep learning methods for protein design☆97Nov 5, 2022Updated 3 years ago
- ☆15Mar 28, 2025Updated 11 months ago
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆32Jan 17, 2023Updated 3 years ago
- Generates consistent PSSM and/or PDB files for protein-protein complexes☆20Jun 26, 2022Updated 3 years ago
- Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile☆72Aug 26, 2024Updated last year
- Some scripts that I keep using over and over.☆21Jul 5, 2025Updated 8 months ago
- Controlling the usage of hydrophobic residues on AfDesign for binder peptide design with AlphaFold hallucination protocol☆33Aug 10, 2023Updated 2 years ago
- Protein hallucination and inpainting with RoseTTAFold☆279Mar 30, 2023Updated 2 years ago
- Neural network model for prediction of amino-acid sequence from a protein backbone structure☆25Mar 5, 2025Updated last year
- All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins☆121May 27, 2025Updated 9 months ago
- ☆91Sep 25, 2024Updated last year
- Python rich client for visual protein Sequence to Structure Analysis☆19Feb 26, 2026Updated last week
- MD DaVis: A python package to analyze molecular dynamics trajectories of proteins☆17Feb 17, 2025Updated last year
- Using Rotamer Interaction Fields from RIFGen/Dock in python☆16May 2, 2021Updated 4 years ago
- Protein design and sculpting using Rosetta and Deep learning methods (RFDiff and Alphafold2)☆50Mar 3, 2026Updated last week
- This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua☆30Sep 17, 2025Updated 5 months ago
- ☆96Oct 14, 2025Updated 4 months ago
- ☆17May 15, 2025Updated 9 months ago
- All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN☆27Mar 3, 2026Updated last week
- Predict multiple protein conformations using sequence clustering and AlphaFold2.☆176Oct 7, 2025Updated 5 months ago
- ☆20Oct 4, 2022Updated 3 years ago
- Generative diverse protein backbones by protein language model☆34Feb 27, 2026Updated last week
- Bayesian Optimization with Pretrained Protein Sequence Models☆56Jul 27, 2024Updated last year
- ☆12Jun 16, 2023Updated 2 years ago
- ☆11May 16, 2020Updated 5 years ago
- ☆11Jan 2, 2021Updated 5 years ago
- The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc…☆13Feb 11, 2026Updated 3 weeks ago