Repository Index

Open source code for AlphaFold 2.

AlphaFold 3 inference pipeline.

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

• drug-discovery
• quantum-chemistry
• deep-learning
• biology

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

Official repository for the Boltz biomolecular interaction models

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

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

• pytorch
• protein-structure
• alphafold2

Code for running RFdiffusion

The repository host gives no description.

This package contains deep learning models and related scripts for RoseTTAFold

Chai-1, SOTA model for biomolecular structure prediction

Code for the ProteinMPNN paper

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

The repository host gives no description.

• foundation-model
• gpt
• single-cell

Biological foundation modeling from molecular to genome scale

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

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

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

🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.

• ai-agents
• bioinformatics
• equity
• genomics

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Precision Medicine Knowledge Graph (PrimeKG)

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

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter