aminoanalytica
- 11 skills
- 0 followers
- 17 hours ago last updated
- ▌ Pymol · aminoanalytica bundleControl PyMOL molecular visualization through Claude Code. Use when asked to "visualize protein", "render structure", "show cartoon", "color by chain", "ray trace", "set up pymol", "install pymol", or work with molecular graphics. Handles setup, visualization commands, and publication-quality figure generation.
- ▌ Rdkit · aminoanalytica bundlePython 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.
- ▌ Biopython · aminoanalytica bundlePython 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.
- ▌ Amina Init · aminoanalytica bundleFoundation skill for autonomous protein engineering via the Amina CLI. Use at session start or after conversation compacting when working with AminoAnalytica's Amina CLI or when you need help using the Amina CLI to do protein engineering tasks like: protein design, structure prediction, binder design, docking, molecular dynamics, enzyme engineering, or any mention of Amina/amina-cli.
- ▌ Scikit Bio · aminoanalytica bundlePython bioinformatics library for sequence manipulation, alignments, phylogenetics, diversity metrics (Shannon, UniFrac), ordination (PCoA, CCA), statistical tests (PERMANOVA, Mantel), and biological file format I/O.
- ▌ Pdb Database · aminoanalytica bundleQuery 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.
- ▌ Chembl Database · aminoanalyticaQuery 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.
- ▌ Biorxiv Database · aminoanalytica bundleSearch and retrieve preprints from bioRxiv. Use when asked to "search bioRxiv", "find preprints", "look up bioRxiv papers", or retrieve life sciences literature.
- ▌ Uniprot Database · aminoanalytica bundleQuery and retrieve protein sequences, annotations, and functional data from UniProt. Supports text search, ID mapping between databases, batch downloads, and access to Swiss-Prot (reviewed) and TrEMBL (predicted) entries.
- ▌ Alphafold Database · aminoanalytica bundleQuery and retrieve AI-predicted protein structures from DeepMind's AlphaFold database. Fetch structures via UniProt accession, interpret pLDDT/PAE confidence scores, and access bulk proteome data for structural biology workflows.
- ▌ Amina De Novo Protein Binder Design · aminoanalytica bundleDe novo protein binder design pipeline -- autonomous backbone generation, sequence design, and multi-metric validation. Use when asked to "design a binder", "create a protein binder", "de novo binder design", "binder for [target]", "design something that binds [protein]", or any task involving computational protein binder engineering from a target structure.