Contrastive learning of protein representations with graph neural networks for structural and functional annotations
☆11Apr 23, 2023Updated 2 years ago
Alternatives and similar repositories for PenLight
Users that are interested in PenLight are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Contrastive fitness learning: Reprogramming protein language models for low-N learning of protein fitness landscape☆36Dec 8, 2025Updated 3 months ago
- to assess structural quality of RNA using 3D CNN☆14Aug 17, 2018Updated 7 years ago
- An official implementation of Protein Representation Learning via Knowledge Enhanced Primary Structure Reasoning☆28Jul 14, 2023Updated 2 years ago
- Code for the paper "OneProt: Towards Multi-Modal Protein Foundation Models"☆22Oct 31, 2025Updated 4 months ago
- ML-optimized library design with improved fitness and diversity for protein engineering☆37Nov 5, 2025Updated 4 months ago
- CLEAN: a contrastive learning model for high-quality functional prediction of proteins☆307Apr 6, 2025Updated 11 months ago
- Method for constructing embeddings of GO terms.☆14Nov 25, 2021Updated 4 years ago
- GCN implementation for RNA-small molecule binding prediction. (https://academic.oup.com/nar/article/48/14/7690/5870337)☆16Nov 28, 2023Updated 2 years ago
- Feature map and function annotation of Proteins☆34Jun 13, 2024Updated last year
- a deep learning architecture for RNA-ligand binding sites prediction☆18Jan 21, 2024Updated 2 years ago
- LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning☆29Jun 4, 2018Updated 7 years ago
- ☆15Mar 25, 2016Updated 9 years ago
- A 3D-equivariant neural network for protein structure accuracy estimation☆22Feb 24, 2023Updated 3 years ago
- ☆15Apr 3, 2025Updated 11 months ago
- Pretrained METL models with minimal dependencies☆17Sep 18, 2025Updated 6 months ago
- Perl scripts for analysis RIC-seq data☆11Feb 6, 2020Updated 6 years ago
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago
- ☆58Aug 28, 2024Updated last year
- ☆69Nov 1, 2022Updated 3 years ago
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated last year
- ☆143Jun 18, 2025Updated 9 months ago
- Decoding the functional networks of non-model organisms☆12Mar 11, 2026Updated last week
- ☆13Oct 19, 2023Updated 2 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
- contrastive learning and pre-trained encoder for protein-ligand binding sites prediction☆37Jul 4, 2025Updated 8 months ago
- Transformer for protein function prediction☆33Oct 24, 2024Updated last year
- Improved ab initio protein structure reconstruction☆15Mar 7, 2018Updated 8 years ago
- GitHub repository for "Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins"☆18Mar 31, 2019Updated 6 years ago
- Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion☆45Jul 27, 2024Updated last year
- NodeCoder is a general framework based on graph convolutional neural network for protein function prediction.☆34May 2, 2024Updated last year
- Steering Vector Repo from "Extracting Latent Steering Vectors from Pretrained Language Models" - ACL2022 Findings☆11Mar 14, 2022Updated 4 years ago
- NetSurfP 3.0: Protein secondary structure and relative solvent accessibility prediction☆24Jun 21, 2023Updated 2 years ago
- ☆15Feb 18, 2025Updated last year
- PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)☆100Mar 18, 2023Updated 3 years ago
- Predict binding affinity of ligand-protein complexes using Graph Neural Networks. The model is implemented using PyTorch Geometric and ba…☆11Nov 26, 2022Updated 3 years ago
- Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/arch…☆10Apr 6, 2023Updated 2 years ago
- High-throughput framework for running molecular simulations for METL☆22Sep 18, 2025Updated 6 months ago
- This is an official implementation for "MMSite: A Multi-modal Framework for the Identification of Active Sites in Proteins".☆18Jan 4, 2025Updated last year
- BertSNR: an interpretable deep learning framework for single nucleotide resolution identification of transcription factor binding sites b…☆13May 27, 2025Updated 9 months ago