[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding
☆151Mar 10, 2025Updated last year
Alternatives and similar repositories for OntoProtein
Users that are interested in OntoProtein are comparing it to the libraries listed below
Sorting:
- DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction☆35Jul 28, 2021Updated 4 years ago
- An official implementation of Protein Representation Learning via Knowledge Enhanced Primary Structure Reasoning☆28Jul 14, 2023Updated 2 years ago
- A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design☆117Mar 3, 2026Updated 2 weeks ago
- GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning, ICLR'2023 (https://arxiv.org/abs/2203.06125)☆317Jun 13, 2025Updated 9 months ago
- [ICML-23 ORAL] ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts☆100Oct 16, 2023Updated 2 years ago
- Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different dom…☆734Dec 11, 2022Updated 3 years ago
- ☆110Mar 7, 2022Updated 4 years ago
- Generative Models for Graph-Based Protein Design☆285Dec 24, 2020Updated 5 years ago
- Transformer-based protein function Annotation with joint feature-Label Embedding☆37Dec 18, 2024Updated last year
- Pre-training Molecular Graph Representation with 3D Geometry, ICLR'22 (https://openreview.net/forum?id=xQUe1pOKPam)☆210Sep 20, 2022Updated 3 years ago
- Unsupervised neural network for learning embeddings of GO terms.☆21Feb 19, 2022Updated 4 years ago
- A Python 3 version of the protein descriptor package propy☆49Feb 8, 2023Updated 3 years ago
- The official implementation of the ICLR'23 paper PiFold: Toward effective and efficient protein inverse folding.☆183Jun 17, 2023Updated 2 years ago
- Code for Fold2Seq paper from ICML 2021☆50May 25, 2022Updated 3 years ago
- Geometric Vector Perceptron --- a rotation-equivariant GNN for learning from biomolecular structure☆164May 1, 2021Updated 4 years ago
- ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit a…☆1,293May 22, 2025Updated 10 months ago
- Exploring Evolution-aware & free protein language models as protein function predictors☆63Sep 28, 2024Updated last year
- ☆244May 22, 2023Updated 2 years ago
- ☆571Apr 3, 2025Updated 11 months ago
- A Text-guided Protein Design Framework, Nat Mach Intell 2025 (https://www.nature.com/articles/s42256-025-01011-z)☆102Jan 11, 2025Updated last year
- ☆256Jul 31, 2024Updated last year
- ☆21Aug 22, 2022Updated 3 years ago
- EquiDock: geometric deep learning for fast rigid 3D protein-protein docking☆256Sep 22, 2023Updated 2 years ago
- PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)☆100Mar 18, 2023Updated 3 years ago
- Evolutionary Scale Modeling (esm): Pretrained language models for proteins☆4,003Feb 7, 2024Updated 2 years ago
- Method for constructing embeddings of GO terms.☆14Nov 25, 2021Updated 4 years ago
- Code for Pre-training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction (https://arxiv.org/abs/2301.12068)☆42Jul 9, 2023Updated 2 years ago
- DeepGO with Fuzzy DL☆33Sep 19, 2022Updated 3 years ago
- A collection of *fold* tools☆302Aug 8, 2025Updated 7 months ago
- 🤡 An up-to-date & curated list of awesome KBQA papers, methods & resources.☆10Jul 14, 2022Updated 3 years ago
- Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure☆318Nov 15, 2025Updated 4 months ago
- EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein☆541Feb 19, 2025Updated last year
- Open-Protein is an open source pre-training platform that supports multiple protein pre-training models and downstream tasks.☆19Apr 14, 2023Updated 2 years ago
- Awesome Protein Representation Learning☆686Nov 16, 2024Updated last year
- Protein Structure Transformer (PST): Endowing pretrained protein language models with structural knowledge☆46Oct 17, 2024Updated last year
- Codes and models for the paper "Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction".☆82Feb 8, 2022Updated 4 years ago
- LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure☆65Mar 4, 2024Updated 2 years ago
- Protein Language Model☆122Jan 15, 2024Updated 2 years ago
- Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures☆49Jan 24, 2022Updated 4 years ago