Repository of Jupyter Notebooks created by the Bio2Byte group
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Updated
May 23, 2024 - Jupyter Notebook
Repository of Jupyter Notebooks created by the Bio2Byte group
An open-source platform for developing protein models beyond AlphaFold.
Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch
RNA, mRNA, DNA, Peptide, Protein, Antibody and Complex | Folding
Screen interactions with AlphaFold-Multimer
AlphaFind: Discover structure similarity across the entire known proteome
molecular graph representation
Stand-alone server for structural proteome curation
Multi-target de novo molecular generator conditioned on AlphaFold's latent protein embeddings.
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
Investigate the role of mtDNA in the sex determination/development of Potamilus streckersoni, a freshwater mussel with doubly uniparental mitochondrial inheritance. Scripts for DESeq2, WGCNA, GSEA, AlphaFold/AlphaPulldown, and mt-sncRNA validation.
The provided code snippet forms a critical component of an automated script aimed at facilitating the prediction of protein structures using the AlphaFold model within a Google Colab environment. The script is tailored to handle the simultaneous upload of multiple input files, each containing multiple protein sequences for prediction.
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