ProtNote is a multimodal deep learning model that leverages free-form text to enable both supervised and zero-shot protein function prediction
☆63Apr 29, 2025Updated last year
Alternatives and similar repositories for protnote
Users that are interested in protnote are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Transformer for protein function prediction (version 2)☆14Jun 5, 2026Updated 2 months ago
- ☆21Sep 19, 2025Updated 10 months ago
- Protein Structure Archiver☆15Sep 10, 2025Updated 11 months ago
- Repository for Protein-Vec, a protein embedding mixture of experts model☆38Jan 24, 2024Updated 2 years ago
- Domain-PFP is a self-supervised method to predict protein functions from the domains☆13Nov 1, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆70Mar 18, 2026Updated 4 months ago
- ☆100Jul 9, 2026Updated last month
- Pooling by PageRank Token Importance. This is a weighted average pooling method where the weights are derived from the internal attention…☆20Jun 11, 2025Updated last year
- 🧬 Augmenting zero-shot mutant prediction by retrieval-based logits fusion. (ISMB/ECCB 2025)☆139Apr 25, 2026Updated 3 months ago
- Detection of remote homology by comparison of protein language model representations☆65Dec 16, 2024Updated last year
- Protein Annotation by Residue-Specific Enrichment: a site-based statistical method for interpretable protein function annotation☆16Jun 16, 2025Updated last year
- Phyla: Towards a Foundation Model for Phylogenetic Inference☆29Nov 20, 2025Updated 8 months ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆127Apr 23, 2026Updated 3 months ago
- PLM-interact: extending protein language models to predict protein-protein interactions.☆72Aug 29, 2025Updated 11 months ago
- 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.
- QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics☆25Jul 1, 2026Updated last month
- This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.☆15Jul 25, 2023Updated 3 years ago
- A drop-in replacement for Rosetta Relax☆30Jan 30, 2026Updated 6 months ago
- ☆22Mar 6, 2024Updated 2 years ago
- ☆40Sep 17, 2024Updated last year
- A protein structure dataset that combines 3D atomic coordinates with biophysical and evolutionary properties for every atom in every "cle…☆39Jul 25, 2024Updated 2 years ago
- CLEAN: a contrastive learning model for high-quality functional prediction of proteins☆323Apr 6, 2025Updated last year
- ☆17Aug 20, 2024Updated last year
- ☆31Dec 12, 2024Updated last year
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. http:…☆155Apr 16, 2025Updated last year
- Metrics to evaluate distributional coverage of generative models of protein structures.☆21Aug 13, 2025Updated 11 months ago
- ☆81Jun 10, 2026Updated last month
- A conditionally adapted protein language model for the generation of enzymes☆24Nov 26, 2024Updated last year
- DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.☆55Jul 22, 2025Updated last year
- 🧬 Fusion of protein sequence and structural information, using denoising pre-training network for zero-shot protein engineering (eLife 2…☆97Jul 20, 2026Updated 3 weeks ago
- Fast deep learning methods for large-scale protein-protein interaction screening☆133Aug 3, 2025Updated last year
- Code and model weights for PoET-2, a retrieval-augmented multimodel protein language model for protein sequence generation and representa…☆27Aug 20, 2025Updated 11 months ago
- ProTrek: illuminating the Protein Universe through Trimodal Protein Language Model (Connecting text and protein)☆212May 15, 2026Updated 2 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.☆23Nov 7, 2025Updated 9 months ago
- Inference code for PoET: A generative model of protein families as sequences-of-sequences☆105Apr 24, 2024Updated 2 years ago
- Phage Annotation using Protein Structures☆170Jul 20, 2026Updated 3 weeks ago
- Code for generating model and predictions for CAFA5 competition 2023 (4th place solution)☆19Updated this week
- All-atom protein generation using latent diffusion, with compositional function and taxonomic prompts. http://bit.ly/plaid-proteins☆127May 27, 2025Updated last year
- A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)☆110Jan 11, 2025Updated last year
- convert alignment bam to pairwise alignment or multiple sequence alignment (msa) at genome specific region☆13May 21, 2024Updated 2 years ago