Agent Skills by PharMolix
Showing 41 vetted skills indexed across 1 GitHub repositories.
PharMolixsingle-cell-atac-seq-peak-calling-annotaion
Call ATAC-seq peaks with MACS2, annotate genomic features, and detect differential accessibility with DESeq2.
PharMolixantibody-structure-prediction-tfold
Predict antibody and nanobody structures from sequences using tfold-based models.
PharMolixretrosynthesis-planning
Plan retrosynthetic routes for complex molecules using AND/OR tree search and vendor validation.
PharMolixdisease-drug-intelligence
Consolidate multi-database evidence to identify innovative drug opportunities for a specified disease.
PharMolixmolecule-biochemical-significance-query-biot5
Query biochemical significance of molecules via BioT5 from SMILES or names.
PharMolixbinding-affinity-prediction-prodigy
Predict protein complex binding affinity scores from PDB structures using Prodigy Prot.
PharMolixstructure-prediction-boltz-2
Predict protein and protein-ligand complex structures and affinities using Boltz-2.
PharMolixtext-based-molecule-editing
Edit molecular structures from natural language prompts using MolT5/BioT5 pipelines.
PharMolixiupac-name-identification-biot5
Identify IUPAC names from SMILES strings or common names using BioT5, MolT5, and RDKit.
PharMolixmutation-design-gfp
Design GFP mutant libraries through iterative optimization and export 96-sequence CSV files.
PharMolixsingle-cell-foundation-model-langcell
Annotates cell identity by aligning embeddings with text descriptions and ontology context.
PharMolixtarget-drug-report
Generate structured drug development reports for specified therapeutic targets.
PharMolixantibody-design-iggm
Design antibodies with IgGM models using antigen PDB data.
PharMolixprotein-function-prediction
Infer protein function and properties from FASTA sequences using BioT5.
PharMolixppi-string-query
Retrieves protein-protein interaction data from the STRING database with confidence scores.
PharMolixsingle-cell-foundation-model-stofm
Preprocess spatial transcriptomics data into hf.dataset and data.h5ad formats.
PharMolixkegg-query
Fetch drug, pathway, and disease data from KEGG REST endpoints.
PharMolixpubchem-query
Query PubChem PUG REST for structures, similar compounds, and bioactivity data.
PharMolixadmet-prediction
Predict ADMET properties from SMILES using GraphMVP ensemble models.
PharMolixbiomed-skill-creator
Create and improve biomedical skills with YAML frontmatter in SKILL.md.
PharMolixcellxgene-census-query
Query CZ CELLxGENE Census data by cell type, tissue, and disease.
PharMolixspatial-transcriptomics-spatial-data-io
Load spatial transcriptomics platform outputs into unified AnnData or SpatialData objects.
PharMolixdrug-drug-interaction-analysis
Analyze drug-drug interactions for up to five medications via KEGG DDI.
PharMolixsimilar-protein-retrieval
Retrieve proteins with similar structure or sequence from UniProt IDs, PDB IDs, FASTA strings, or PDB files.