Tokenvizz is a newly developed tool designed for genomic data discovery and visualization, leveraging Graph Retrieval-Augmented Generation (GraphRAG) inspired tokenization and graph-based modeling. It employs innovative tokenization methods, including single nucleotide tokenization and byte-pair encoding (BPE) from the DNABERT2 model, alongside non-overlapping k-mer tokenization from the Nucleotide Transformer. In Tokenvizz, genomic sequences are represented as graphs, with sequence k-mers serving as nodes and attention scores as edge weights, facilitating the visual interpretation of complex, non-linear relationships within DNA sequences. Additionally, research utilizing AlphaFold2 has expanded to predict structural conformations of peptides, using a dataset of 557 peptides, marking a significant advancement in peptide analysis. AlphaFold3 has also been evaluated for its accuracy in predicting ligand-bound G protein-coupled receptor (GPCR) structures, showing improvements in overall architecture accuracy.
AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors 1. This study evaluates AlphaFold3’s (AF3) ability to predict ligand-bound GPCR structures, finding improvements in overall GPCR architecture accuracy compared to… https://t.co/puN6oxD1Mj
Prediction of peptide structural conformations with AlphaFold2 1. This study extends the capabilities of AlphaFold2 (AF2) to predict structural conformations of peptides, a domain previously unexplored compared to proteins. 2. Using a dataset of 557 peptides with nuclear… https://t.co/UZu34519IB
Prediction of peptide structural conformations with AlphaFold2 https://t.co/VTlbqOAleF #biorxiv_bioinfo