protein-embedding

Awesome Protein Representation Learning

Code for ICLR 2024 (Spotlight) paper "MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding"

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

Multi-task and masked language model-based protein sequence embedding models.

Simple python interface for the OpenProtein.AI REST API.

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted sequence properties and eliminates the need to manually extract and select features from phage sequences

Published in Bioinformatics. Phage-host interaction prediction tool that incorporates protein structure information in representing receptor-binding proteins (RBPs). It improves performance especially for phages with RBPs that have low sequence similarity to those of known phages

Generation Co-expression Network Embeddings (CxNEs) for plant genes using Graph Attention Networks (GAT))

Code for Binding Affinity Prediction with Graph Neural Networks

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