Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
Fast indexing and search of discontinuous motifs in protein structures
MMseqs2 app to run on your workstation or servers
A NumPy port of the foldseek code for encoding protein structures to 3di.
Bioinformatics protocol that aims at mining information at the sequence and structure level of protein chain to detect possible evolutionary conserved residues.
Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.
Analysis workflow for novel gene search based on structural similarity search
Visualizing 3D fragments of proteins in a scatterplot using Foldseek's 3Di and Transformers.
GUI and CLI workflow for phylogenetic tree construction, tanglegram comparison, and optional Foldseek protein-structure similarity.
Enable multi-AI collaboration to streamline novel writing with slash commands for planning, drafting, reviewing, and managing story workflows in Claude Code.
Many-to-many protein search and querying with Foldseek
StruSel: Structurome-wide Selectivity of pathogen-exclusive targets
Rooted, dual-method (ML + Bayesian) phylogeny of the bacterial Hfq family, with archaeal SmAP outgroup rooting and ESMFold/Foldseek structural verification
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