A NumPy port of the foldseek code for encoding protein structures to 3di.
☆80Aug 22, 2025Updated 6 months ago
Alternatives and similar repositories for mini3di
Users that are interested in mini3di are comparing it to the libraries listed below
Sorting:
- NEFF Calculator and MSA File Converter☆13Sep 16, 2025Updated 5 months ago
- Fast protein domain structure embedding+search tool☆27Sep 21, 2025Updated 5 months ago
- PyO3 bindings and Python interface to sylph, an ultrafast method for containment ANI querying and taxonomic profiling.☆20Dec 12, 2024Updated last year
- A Python interface to gb-io, a fast GenBank parser written in Rust.☆24Feb 23, 2026Updated last week
- Fast protein structure searching or your money back☆118Jan 14, 2026Updated last month
- Repository for Fast Non-autoregressive Inverse Folding with Discrete Diffusion☆18Feb 8, 2024Updated 2 years ago
- A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.☆21Nov 25, 2025Updated 3 months ago
- Terminal viewer for pdb files☆21Jan 5, 2026Updated last month
- Code release for "Improving diffusion-based protein backbone generation with global-geometry-aware latent encoding"☆47Aug 5, 2025Updated 7 months ago
- ☆17Jun 13, 2025Updated 8 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
- ☆15Mar 28, 2025Updated 11 months ago
- Fast indexing and search of discontinuous motifs in protein structures☆121Feb 24, 2026Updated last week
- ☆22Nov 6, 2024Updated last year
- Comparison pipeline for Prokaryote Protein Coding Gene Predictors☆28Feb 12, 2026Updated 2 weeks ago
- Bilingual Language Model for Protein Sequence and Structure☆301Jan 2, 2025Updated last year
- A model-context-protocol server for molecules.☆89Apr 20, 2025Updated 10 months ago
- ☆17Aug 28, 2025Updated 6 months ago
- Sketch phylogenetic trees and networks☆24Feb 5, 2026Updated last month
- Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)☆74Feb 24, 2025Updated last year
- ☆57Jul 22, 2025Updated 7 months ago
- Public version for Distance-AF☆30Aug 17, 2025Updated 6 months ago
- Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information☆32Jan 22, 2026Updated last month
- GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts☆36Apr 16, 2024Updated last year
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Nov 14, 2023Updated 2 years ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆85Nov 13, 2025Updated 3 months ago
- DeepGO with Fuzzy DL☆32Sep 19, 2022Updated 3 years ago
- Compressing protein structures effectively with torsion angles☆188Feb 10, 2026Updated 3 weeks ago
- Nail is an Alignment Inference tooL☆55Feb 21, 2026Updated last week
- Versatile computational pipeline for processing protein structure data for deep learning applications.☆274Feb 14, 2024Updated 2 years ago
- A lightweight platform-accelerated library for biological motif scanning using position weight matrices.☆62Updated this week
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆123Jan 16, 2026Updated last month
- Reference-free Binning of Metagenomics Long Reads using Coverage and Composition☆20Sep 10, 2024Updated last year
- Python package to plot a phylogenetic tree on an existing matplotlib axis.☆27Jul 21, 2025Updated 7 months ago
- ☆87Nov 18, 2025Updated 3 months ago
- k-mers and the like☆22Updated this week
- ☆24Aug 25, 2023Updated 2 years ago
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆21Jun 6, 2024Updated last year
- ☆24May 19, 2025Updated 9 months ago