Open source code for AlphaFold 2.
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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
Biomni: a general-purpose biomedical AI agent
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
- tensorflow
- deep-neural-network
- genomics
- science
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Making Protein folding accessible to all!
- bioinformatics
- multiple-sequence-alignment
- protein-structure
- structure-prediction
R toolkit for single cell genomics
- human-cell-atlas
- single-cell-rna-seq
- single-cell-genomics
- cran
NeuroKit2: The Python Toolbox for Neurophysiological Signal Processing
- python
- ecg
- eda
- emg
Toward High-Accuracy Open-Source Biomolecular Structure Prediction.
- ai4science
- research
Chai-1, SOTA model for biomolecular structure prediction
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
- bioinformatics
- sequence-alignment
- genomics
- fm-index
Implementation of Alphafold 3 from Google Deepmind in Pytorch
- artificial-intelligence
- deep-learning
- attention-mechanisms
- denoising-diffusion
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
- artificial-intelligence
- deep-learning
- protein-folding
- attention-mechanism
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
An open-source application for biological image analysis
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
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
Fast, sensitive and accurate integration of single-cell data with Harmony
Sequential regulatory activity predictions with deep convolutional neural networks.
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations