A NumPy port of the foldseek code for encoding protein structures to 3di.
☆82Aug 22, 2025Updated 9 months ago
Alternatives and similar repositories for mini3di
Users that are interested in mini3di are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆21Dec 12, 2024Updated last year
- Fast protein domain structure embedding+search tool☆30Sep 21, 2025Updated 8 months ago
- A Python interface to gb-io, a fast GenBank parser written in Rust.☆24May 21, 2026Updated 3 weeks ago
- NEFF Calculator and MSA File Converter☆14May 6, 2026Updated last month
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆23Nov 25, 2025Updated 6 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Code for generating model and predictions for CAFA5 competition 2023 (4th place solution)☆19May 24, 2024Updated 2 years ago
- Repository for Fast Non-autoregressive Inverse Folding with Discrete Diffusion☆18Feb 8, 2024Updated 2 years ago
- Fast protein structure searching or your money back☆119Apr 13, 2026Updated 2 months ago
- ☆18Aug 28, 2025Updated 9 months ago
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆28Feb 12, 2026Updated 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
- Fast indexing and search of discontinuous motifs in protein structures☆178Jun 8, 2026Updated last week
- Code release for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding"☆48Aug 5, 2025Updated 10 months ago
- ☆22Nov 6, 2024Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Bilingual Language Model for Protein Sequence and Structure☆310Mar 6, 2026Updated 3 months ago
- Terminal viewer for pdb files☆22Jan 5, 2026Updated 5 months ago
- ☆60Jul 22, 2025Updated 10 months ago
- ☆15Mar 28, 2025Updated last year
- Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information☆33Jan 22, 2026Updated 4 months ago
- A model-context-protocol server for molecules.☆94Apr 20, 2025Updated last year
- ☆10Jun 9, 2025Updated last year
- Compressing protein structures effectively with torsion angles☆194Feb 10, 2026Updated 4 months ago
- ☆18Jun 13, 2025Updated last year
- 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.
- Nail is an Alignment Inference tooL☆61May 14, 2026Updated last month
- Public version for Distance-AF☆32Aug 17, 2025Updated 9 months ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆126Apr 23, 2026Updated last month
- DeepGO with Fuzzy DL☆34Sep 19, 2022Updated 3 years ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- Code associated with the paper "Exploring and Mapping Chemical Space with Molecular Assembly Trees"☆24Sep 29, 2021Updated 4 years ago
- ☆24May 19, 2025Updated last year
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆88Mar 12, 2026Updated 3 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Predict the structure of immune receptor proteins☆182Nov 11, 2025Updated 7 months ago
- Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)☆80May 27, 2026Updated 2 weeks ago
- ☆18Jun 1, 2026Updated 2 weeks ago
- A Python Tool for Benchmarking Ontological Classification Methods☆53Jan 19, 2026Updated 4 months ago
- Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and …☆10Jun 19, 2019Updated 6 years ago
- Foldseek enables fast and sensitive comparisons of large structure sets.☆1,248May 13, 2026Updated last month
- ☆135Aug 29, 2024Updated last year