Protein Sequence Design with Deep Learning and Tooling like Monte Carlo Sampling and Analysis
☆62Oct 28, 2025Updated 10 months ago
Alternatives and similar repositories for timed-design
Users that are interested in timed-design are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆18Mar 13, 2024Updated 2 years ago
- Structure-conditioned masked language modeling for protein sequence design☆74Jan 31, 2024Updated 2 years ago
- DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.☆31Mar 4, 2025Updated last year
- Deep learning framework for protein sequence design from a backbone scaffold that can leverage the molecular context including non-protei…☆50Nov 4, 2025Updated 10 months ago
- ☆47Sep 16, 2024Updated last year
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- A compilation of deep learning methods for protein design☆95Nov 5, 2022Updated 3 years ago
- This repository contains code for the paper: "Tertiary motifs as building blocks for the design of protein-binding peptides"☆20Jan 15, 2024Updated 2 years ago
- Fast protein structure searching or your money back☆119Apr 13, 2026Updated 4 months ago
- Implementation of Protein Invariant Point Packer (PIPPack)☆37May 28, 2024Updated 2 years ago
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆33Jan 17, 2023Updated 3 years ago
- Code for our paper "Protein sequence design with a learned potential"☆81Sep 8, 2023Updated 3 years ago
- ☆15Mar 28, 2025Updated last year
- Code for our paper "Protein sequence design with a learned potential"☆34Aug 5, 2021Updated 5 years ago
- Using Rotamer Interaction Fields from RIFGen/Dock in python☆17May 2, 2021Updated 5 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Some scripts that I keep using over and over.☆21Jul 5, 2025Updated last year
- This repository contains a set of scripts for performing singular value decomposition on protein multiple sequence alignments, and analyz…☆11Aug 12, 2024Updated 2 years ago
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆68Aug 11, 2026Updated 3 weeks ago
- Protein design and sculpting using Rosetta and Deep learning methods (RFDiff and Alphafold2)☆71Updated this week
- ☆19Oct 4, 2022Updated 3 years ago
- Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile☆72Apr 13, 2026Updated 4 months ago
- ☆101Jul 24, 2026Updated last month
- Protein hallucination and inpainting with RoseTTAFold☆285Mar 30, 2023Updated 3 years ago
- HalluDesign, a hallucination-driven all-atom framework for the iterative co-optimization and co-design of protein sequences and structure…☆90Jul 23, 2026Updated last month
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Neural network model for prediction of amino-acid sequence from a protein backbone structure☆25Mar 5, 2025Updated last year
- ☆92Sep 25, 2024Updated last year
- Physical energy function for protein sequence design☆44May 6, 2023Updated 3 years ago
- ☆16Sep 29, 2025Updated 11 months ago
- Controlling the usage of hydrophobic residues on AfDesign for binder peptide design with AlphaFold hallucination protocol☆31Aug 10, 2023Updated 3 years ago
- Bayesian Optimization with Pretrained Protein Sequence Models☆56Jul 27, 2024Updated 2 years ago
- Rosetta Funclib☆25May 9, 2020Updated 6 years ago
- Template-based protein design with Raygun☆151Jul 30, 2026Updated last month
- Protein Structure Archiver☆15Sep 10, 2025Updated 11 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- ☆74Feb 13, 2026Updated 6 months ago
- Generates consistent PSSM and/or PDB files for protein-protein complexes☆20Jun 26, 2022Updated 4 years ago
- ☆37Oct 16, 2024Updated last year
- Code for holographic machine learning of proteins☆25Oct 29, 2024Updated last year
- A collection of *fold* tools☆303Aug 8, 2025Updated last year
- Structure prediction and design of proteins with noncanonical amino acids☆146Feb 1, 2026Updated 7 months ago
- All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins☆126May 27, 2025Updated last year