☆110Mar 7, 2022Updated 3 years ago
Alternatives and similar repositories for meaningful-protein-representations
Users that are interested in meaningful-protein-representations are comparing it to the libraries listed below
Sorting:
- Homology reduced UniProt, train-/valid-/testsets for language modeling☆16Apr 20, 2022Updated 3 years ago
- Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different dom…☆732Dec 11, 2022Updated 3 years ago
- a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)☆89Jul 6, 2023Updated 2 years ago
- [ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding☆151Mar 10, 2025Updated 11 months ago
- Prediction of binding residues for metal ions, nucleic acids, and small molecules.☆34Sep 2, 2025Updated 5 months ago
- DistilProtBert implementation, a distilled version of ProtBert model.☆16Sep 21, 2022Updated 3 years ago
- ☆255Jul 31, 2024Updated last year
- Protein sequence classification with self-supervised pretraining☆82Nov 29, 2021Updated 4 years ago
- Learning Protein Constitutive Motifs from Sequence Data: RBM toolbox☆20Jan 30, 2019Updated 7 years ago
- Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer ann…☆41Aug 29, 2025Updated 6 months ago
- Web cards/apps describing peptides☆30Apr 26, 2023Updated 2 years ago
- Nextflow pipeline for the computation of structure-based MSAs with AlphaFold2 models☆12Dec 20, 2022Updated 3 years ago
- Modelling the Language of Life - Deep Learning Protein Sequences☆76Dec 28, 2020Updated 5 years ago
- Evolutionary velocity with protein language models☆97Dec 9, 2025Updated 2 months ago
- Get protein embeddings from protein sequences☆506Apr 28, 2023Updated 2 years ago
- A collection of *fold* tools☆302Aug 8, 2025Updated 6 months ago
- Efficient evolution from protein language models☆220Aug 26, 2023Updated 2 years ago
- pretrained LookingGlass language model for biological read-length DNA sequences, and related models derived from transfer learning☆15Feb 19, 2026Updated last week
- Python package to manage protein structures and their annotations☆45Feb 22, 2024Updated 2 years ago
- AutoGraph: autonomous graph based clustering of metabolite conformations☆12Mar 25, 2022Updated 3 years ago
- ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit a…☆1,291May 22, 2025Updated 9 months ago
- open source repository☆146Nov 30, 2023Updated 2 years ago
- A generative latent variable model for biological sequence families.☆247Mar 15, 2022Updated 3 years ago
- Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.☆60Mar 24, 2021Updated 4 years ago
- Listing of papers about machine learning for proteins.☆1,688May 31, 2024Updated last year
- Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019☆262Jun 16, 2021Updated 4 years ago
- Retrieved Sequence Augmentation for Protein Representation Learning☆53Nov 1, 2023Updated 2 years ago
- A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design☆111Sep 30, 2024Updated last year
- This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"☆14Jun 7, 2023Updated 2 years ago
- DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction☆35Jul 28, 2021Updated 4 years ago
- Multi-task and masked language model-based protein sequence embedding models.☆106Jun 16, 2021Updated 4 years ago
- Inference code for PoET: A generative model of protein families as sequences-of-sequences☆93Apr 24, 2024Updated last year
- Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix☆35Jul 28, 2022Updated 3 years ago
- ☆23Nov 14, 2025Updated 3 months ago
- ☆19Oct 8, 2020Updated 5 years ago
- ☆20Jul 16, 2025Updated 7 months ago
- Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."☆305May 1, 2025Updated 9 months ago
- DomainMapper is a parser for hmmscan full output files built centrally around ECOD domain definitions. Users can optimize DomainMapper's …☆13Dec 13, 2023Updated 2 years ago
- BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models☆14Aug 21, 2022Updated 3 years ago