Contrastive learning of protein representations with graph neural networks for structural and functional annotations
☆11Apr 23, 2023Updated 3 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☆37Dec 8, 2025Updated 7 months ago
- An official implementation of Protein Representation Learning via Knowledge Enhanced Primary Structure Reasoning☆28Jul 14, 2023Updated 3 years ago
- to assess structural quality of RNA using 3D CNN☆15Aug 17, 2018Updated 7 years ago
- ML-optimized library design with improved fitness and diversity for protein engineering☆37Nov 5, 2025Updated 8 months ago
- CLEAN: a contrastive learning model for high-quality functional prediction of proteins☆320Apr 6, 2025Updated last year
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Method for constructing embeddings of GO terms.☆14Nov 25, 2021Updated 4 years ago
- ARES implement in PyTorch☆17Feb 27, 2024Updated 2 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☆35Jun 13, 2024Updated 2 years ago
- a deep learning architecture for RNA-ligand binding sites prediction☆18Jan 21, 2024Updated 2 years ago
- Python Scripts for Bioinformatics☆15Apr 24, 2024Updated 2 years ago
- Embeddings to Network Alignment - align biological networks between two species☆10Sep 8, 2023Updated 2 years ago
- ☆15Mar 25, 2016Updated 10 years ago
- LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning☆29Jun 4, 2018Updated 8 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A 3D-equivariant neural network for protein structure accuracy estimation☆22Feb 24, 2023Updated 3 years ago
- Code for the paper "OneProt: Towards Multi-Modal Protein Foundation Models"☆24Jun 30, 2026Updated 3 weeks ago
- Pretrained METL models with minimal dependencies☆16Sep 18, 2025Updated 10 months ago
- Perl scripts for analysis RIC-seq data☆11Feb 6, 2020Updated 6 years ago
- contrastive learning and pre-trained encoder for protein-ligand binding sites prediction☆37Jul 4, 2025Updated last year
- 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
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago
- ☆57Aug 28, 2024Updated last year
- ☆145Jun 18, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- ☆68Nov 1, 2022Updated 3 years ago
- ☆13Oct 19, 2023Updated 2 years ago
- Perform file-based malware scan on your on-prem servers with AWS☆14Oct 31, 2023Updated 2 years ago
- structRFM: A fully open structure-guided RNA foundation model for robust structural and functional inference☆35Jun 11, 2026Updated last month
- Transformer for protein function prediction☆34Oct 24, 2024Updated last year
- Improved ab initio protein structure reconstruction☆15Mar 7, 2018Updated 8 years ago
- Command-line tools for protein structure analysis: convert PDB, mmCIF, PDBML, or XYZR files into atomic sphere data, then compute volumes…☆15Apr 16, 2026Updated 3 months ago
- Decoding the functional networks of non-model organisms☆12May 10, 2026Updated 2 months ago
- Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer ann…☆41Aug 29, 2025Updated 10 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion☆45Jul 27, 2024Updated last year
- Steering Vector Repo from "Extracting Latent Steering Vectors from Pretrained Language Models" - ACL2022 Findings☆11Mar 14, 2022Updated 4 years ago
- NodeCoder is a general framework based on graph convolutional neural network for protein function prediction.☆33May 2, 2024Updated 2 years ago
- BertSNR: an interpretable deep learning framework for single nucleotide resolution identification of transcription factor binding sites b…☆13May 27, 2025Updated last year
- PEER Benchmark, appear at NeurIPS 2022 Dataset and Benchmark Track (https://arxiv.org/abs/2206.02096)☆104Mar 18, 2023Updated 3 years ago
- Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/arch…☆11Apr 6, 2023Updated 3 years ago
- ☆13Oct 25, 2025Updated 8 months ago