uniprot-database
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rdkit
Python cheminformatics library for molecular manipulation and analysis. Parse SMILES/SDF/MOL formats, compute descriptors (MW, LogP, TPSA), generate fingerprints (Morgan, MACCS), perform substructure queries with SMARTS, create 2D/3D geometries, calculate similarity, and run chemical reactions.
28biorxiv-database
Search and retrieve preprints from bioRxiv. Use when asked to "search bioRxiv", "find preprints", "look up bioRxiv papers", or retrieve life sciences literature.
28scikit-bio
Python bioinformatics library for sequence manipulation, alignments, phylogenetics, diversity metrics (Shannon, UniFrac), ordination (PCoA, CCA), statistical tests (PERMANOVA, Mantel), and biological file format I/O.
28pdb-database
Query and retrieve protein/nucleic acid structures from RCSB PDB. Use when you need to search the PDB database for structures or metadata. Supports text, sequence, and structure-based searches, coordinate downloads, and metadata retrieval for structural biology workflows.
28biopython
Python toolkit for computational biology. Use when asked to "parse FASTA", "read GenBank", "query NCBI", "run BLAST", "analyze protein structure", "build phylogenetic tree", or work with biological sequences. Handles sequence I/O, database access, alignments, structure analysis, and phylogenetics.
28chembl-database
Query the ChEMBL database for bioactive compounds, drug targets, and bioactivity data. Use this skill when searching for small molecules, finding inhibitors for protein targets, or analyzing drug mechanisms of action.
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