Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Repository Index
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Chai-1, SOTA model for biomolecular structure prediction
Biological foundation modeling from molecular to genome scale
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
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
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
R package for detecting doublets in single-cell RNA sequencing data
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Reference mapping for single-cell genomics
- single-cell
- deep-learning
- rna-seq-analysis
- data-integration
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
Open Frontier Biomolecular Intelligence
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
Bi-Directional Equivariant Long-Range DNA Sequence Modeling
MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
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