Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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DeepChem github.com
Deep learning library for drug discovery, quantum chemistry, and materials science.
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BioGPT github.com
paper - A GPT-2 model pre-trained on 15 million PubMed abstracts, along with fine-tuned versions for several biomedical tasks.
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rdkit github.com
Cheminformatics software & machine learning toolkit.
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AlphaFold3 github.com
Predicts structures of proteins, nucleic acids, small molecules, and their complexes.
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Agent Laboratory github.com
End-to-end multi-agent research workflow for literature review, experimentation, implementation, analysis, and report generation.
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Evo 2 github.com
Genome foundation model trained on 9 trillion DNA base pairs across all domains of life with a 1M-token context window and single-nucleotide resolution.
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Boltz-1 github.com
Open-source all-atom biomolecular structure prediction model for proteins, nucleic acids, small molecules, and their complexes achieving AlphaFold3-level accuracy.
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Evolutionary Scale Modeling (ESM) github.com
Protein embeddings.
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Biomni github.com
General-purpose biomedical AI agent integrating planning, code execution, specialized tools, databases, and software across diverse biomedical research tasks.
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Paper2Agent github.com
Multi-agent system that transforms research papers and associated code into interactive, testable scientific agents and MCP tools.
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OpenFold github.com
Trainable, memory-efficient open-source reproduction of AlphaFold2 enabling custom protein structure prediction workflows.
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RFdiffusion github.com
Generative model for protein backbone design using diffusion.
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ESM3 github.com
Multimodal protein language model that jointly reasons over sequence, structure, and function for generative protein design and engineering.
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ESM Cambrian (ESM C) github.com
Protein representation foundation-model family designed as an efficient next-generation successor to ESM2, spanning 300M to multi-billion-parameter models.
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RoseTTAFold github.com
Three-track neural network for protein structure prediction.
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STAR github.com
Ultrafast universal RNA-seq aligner with support for spliced alignment and single-cell quantification via STARsolo.
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AlphaGenome github.com
Long-context DNA model predicting multimodal regulatory outputs including expression, splicing, chromatin features, and contact maps at near base-pair resolution.
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Protenix github.com
Trainable biomolecular structure-prediction framework for proteins, nucleic acids, ligands, and complexes with open training and inference pipelines.
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Chai-1 github.com
Unified molecular structure prediction model covering proteins, nucleic acids, small molecules, and complexes.
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ProteinMPNN github.com
Deep learning model for protein sequence design given backbone structure.
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ToolUniverse github.com
Unified scientific tool ecosystem for building AI scientists that can discover, select, and execute biomedical tools and databases.
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totalVI github.com
Probabilistic framework for joint analysis of paired scRNA-seq and protein (CITE-seq) data enabling multi-modal cell state representation across single-cell datasets.
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scGPT github.com
Transformer-based foundation model pretrained on millions of single-cell profiles.
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DiffDock github.com
Diffusion generative model for molecular docking, predicting the binding pose of small molecules to protein targets.
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Evo github.com
Long-context genomic foundation model (up to 1M tokens).
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Hetionet: an integrative network of disease github.com
Heterogeneous network integrating genes, diseases, drugs, pathways, and more.
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ProtTrans github.com
Suite of protein language models (ProtBERT, ProtT5, ProtXLNet) trained on billions of protein sequences from UniRef and BFD.
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mol2vec github.com
Unsupervised molecular embedding method inspired by Word2Vec for learning vector representations of chemical substructures.
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DeepPurpose github.com
Deep learning library for drug repurposing.
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Uni-Mol github.com
3D molecular pretraining framework for universal representation learning on molecules and protein pockets.
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