Repository Index

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

Chai-1, SOTA model for biomolecular structure prediction

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

Sequential regulatory activity predictions with deep convolutional neural networks.

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

RNA-seq prediction with deep convolutional neural networks.

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

A Network Integration Approach for Drug-Target Interaction Prediction

MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning

code to run sei and obtain sei and sequence class predictions

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

TypeDB Bio: Biomedical Knowledge Graph

• bioinformatics
• knowledge-graph
• knowledge-base
• drug-discovery

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies