TurtleTools / geometricusLinks
A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.
☆41Updated 2 years ago
Alternatives and similar repositories for geometricus
Users that are interested in geometricus are comparing it to the libraries listed below
Sorting:
- Fast and accurate protein structure prediction☆56Updated 10 months ago
- Prediction of binding residues for metal ions, nucleic acids, and small molecules.☆34Updated 3 months ago
- ☆44Updated last year
- Graph Network for protein-protein interface including language model features☆33Updated last year
- Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer ann…☆38Updated 3 months ago
- Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.☆34Updated 3 years ago
- ML toolset for creating TED: The Encyclopedia of Domains☆24Updated 6 months ago
- ☆32Updated 2 months ago
- A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence☆60Updated 8 months ago
- Repository for Protein-Vec, a protein embedding mixture of experts model☆38Updated last year
- ☆23Updated 3 weeks ago
- Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".☆59Updated 4 years ago
- We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original represe…☆20Updated 2 years ago
- Code, intermediate results and an interactive visualisation on prediction of putative novel enzymes and small molecule binding proteins p…☆27Updated 2 years ago
- Python package to atom map, correct and suggest enzymatic reactions☆39Updated last year
- ☆36Updated 10 months ago
- Learning Protein Constitutive Motifs from Sequence Data: RBM toolbox☆20Updated 6 years ago
- A software-suite to perform multiple protein structure alignment and structure feature extraction.☆31Updated 2 years ago
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆30Updated 2 years ago
- ☆74Updated last year
- Evolutionary velocity with protein language models☆94Updated this week
- Machine learning prediction of enzyme optimum pH☆48Updated 7 months ago
- 2D portraits of 3D protein structures☆27Updated 2 months ago
- Python package to manage protein structures and their annotations☆45Updated last year
- A NumPy port of the foldseek code for encoding protein structures to 3di.☆76Updated 3 months ago
- Fork of matteofigliuzzi/bmDCA repository for Boltzmann-machine Direct Coupling Analysis (bmDCA).☆35Updated 5 years ago
- Ultra-fast in-silico structure mutation☆35Updated 7 months ago
- Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."☆70Updated last year
- ☆31Updated last year
- The DSSP building software☆47Updated 2 years ago