skills_overview.md

BioMedSkills Overview

This document provides a comprehensive overview of all available skills in the OpenBioMed toolkit.

Last Updated: 2026-03-19

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Skills Summary

Total Skills
45

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All Skills

Biochemistry & Drug Discovery

Name	Category	Usage	Status
drug-candidate-discovery	Drug Discovery	Generate diverse druggable molecules for a given target or disease using AI-powered drug discovery tools including target identification, structure retrieval, and molecule generation.
drug-lead-analysis	Drug Discovery	Analyze drug candidate molecules for drug-likeness (QED, Lipinski), ADMET properties, BBB penetration, and safety profiles.	Recommended
target-based-lead-design	Drug Discovery	Generate diverse lead compounds for a specific protein target using structure-based drug design with MolCraft. Includes docking, ADMET filtering, diversity selection, and iterative refinement.	Recommended
admet-prediction	ADMET Prediction	Predict comprehensive ADMET properties (BBB penetration, side effects, Caco-2 permeability, half-life, LD50 toxicity) for drug candidates using GraphMVP ensemble models.	Recommended
retrosynthesis-planning	Synthetic Chemistry	Expert-in-the-loop retrosynthetic planning workflow for breaking down target molecules into available starting materials and designing synthetic routes with AiZynthFinder integration.	Recommended
iupac-name-identification-biot5	Drug Discovery	Identify the IUPAC name of a molecule using BioT5 question answering model.
molecule-biochemical-significance-query-biot5	Multi-Modal Reasoning	Query a molecule's biochemical significance and roles in biology and chemistry using BioT5 multi-modal model.
text-based-molecule-editing	Drug Discovery	Modify molecules based on natural language descriptions using MolT5/BioT5 models for property optimization (solubility, potency, drug-likeness).
target-drug-report	Drug Discovery	Generate comprehensive drug development progress reports for disease therapeutic targets with 7 analysis sections including clinical pipeline, research trends, and patent landscape.
disease-drug-intelligence	Drug Discovery	Analyze disease-to-innovative-drug relationships by querying multiple databases (ChEMBL, ClinicalTrials) to generate comprehensive Chinese reports on disease-target-drug pipelines.
drug-drug-interaction-analysis	Safety/Toxicology	Analyze potential drug-drug interactions (DDI) for up to 5 drugs using KEGG DDI database with severity levels and mechanism analysis.

Protein Analysis & Engineering

Name	Category	Usage	Status
protein-mutation-analysis	Mutation Analysis	Analyze protein mutations by retrieving protein data, explaining mutation effects with MutaPLM, predicting structure with ESMFold, and visualizing results.	Recommended
mutation-design-aav	Mutation Analysis	Design high-fitness and high-diversity mutants of AAV VP1 capsid protein through multi-round iterative optimization.
mutation-design-gfp	Mutation Analysis	Design high-fluorescence and high-diversity GFP mutants through multi-round iterative optimization.
functional-protein-design	Protein Engineering	Generate functional protein sequences using CodeFP with Gene Ontology (GO) tag guidance for de novo protein design.
protein-function-prediction	Protein Engineering	Predict protein function and properties from amino acid sequences using BioT5 for functional annotation and pathway analysis.
similar-protein-retrieval	Data Retrieval	Retrieve proteins with similar structures (FoldSeek) or sequences (MSA) from UniProt, PDB, and AFDB databases.	Recommended
structure-prediction-boltz-2	Structure Prediction	Predict protein complex structures and protein-ligand complexes with binding affinity (IC50) using Boltz-2.
protein-structure-design-boltzgen	Structure Design	All-atom protein design using BoltzGen diffusion model for binder design, peptide design, and small molecule binding design.
antibody-structure-prediction-tfold	Structure Prediction	Predict antibody/nanobody structures and antigen-antibody complex structures using tFold model.
antibody-design-iggm	Antibody Design	Epitope-conditioned de novo antibody design and affinity maturation using IgGM model.
binding-affinity-prediction-prodigy	Binding Analysis	Predict binding affinity scores for protein complexes using Prodigy from structure files.	Recommended
protein-ligand-binding-analysis-plip	Binding Analysis	Analyze protein-ligand interactions in PDB structures using PLIP for hydrogen bonds, hydrophobic contacts, π-stacking, salt bridges, and visualization.
protein-subcellular-localization-prediction-biot5	Protein Engineering	Predict protein subcellular localization (nucleus, cytoplasm, membrane, etc.) from amino acid sequences using BioT5 model.

Single-Cell Omics Data Analysis

Name	Category	Usage	Status
single-cell-foundation-model-scrna-seq-geneformer	Foundation Model	Geneformer workflows for tokenization, cell/gene classification, embedding extraction, and in silico perturbation analysis.	Recommended
single-cell-foundation-model-scrna-seq-langcell	Foundation Model	LangCell for zero-shot and few-shot cell type annotation with multimodal cell-text matching.	Recommended
single-cell-foundation-model-scrna-seq-scgpt	Foundation Model	scGPT for preprocessing, binning, cell embedding extraction, fine-tuning, and reference mapping workflows.	Recommended
spatial-transcriptomics-foundation-model-stofm	Foundation Model	SToFM for spatial transcriptomics preprocessing, cell embedding generation with SE(2) Transformer, and downstream analysis.	Recommended
single-cell-scrna-seq-analysis-scanpy	Bioinformatics	Complete scRNA-seq analysis workflow with Scanpy including QC, normalization, dimensionality reduction, clustering, and marker gene identification.
single-cell-multi-omics-analysis-scvi	Bioinformatics	Probabilistic deep learning for single-cell multi-omics analysis including scVI, scANVI, totalVI, and spatial deconvolution.
cellxgene-census-query	Data Query	Query CZ CELLxGENE Census (61M+ cells) for single-cell expression data by cell type, tissue, or disease.
spatial-transcriptomics-spatial-data-io	Data I/O	Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.
single-cell-atac-seq-qc-processing	ATAC-seq	Trim adapters, align reads, remove duplicates and mitochondrial contamination, and evaluate chromatin accessibility data quality. Includes TSS enrichment scoring and fragment size analysis.
single-cell-atac-seq-peak-calling-annotaion	ATAC-seq	Call accessible chromatin peaks with MACS2, annotate peaks to genomic features and genes, and identify differentially accessible regions (DARs) between conditions.
single-cell-proteomics-data-processing	Mass Spectrometry	Load, inspect, centroid, and extract features from raw LC-MS/MS data files using pyOpenMS. Includes TIC plotting, feature detection, and format conversion.
single-cell-proteomics-peptide-identification	Mass Spectrometry	Search MS2 spectra against protein databases with MSFragger/Comet, apply target-decoy FDR filtering, and perform protein inference with parsimony principle.
single-cell-multi-omics-data-harmonization	Data Integration	Prepare multi-omics datasets (RNA-seq, proteomics, methylation) for joint integration with per-assay normalization, batch correction, feature ID alignment, and missing value handling.

Data Retrieval & Knowledge

Name	Category	Usage	Status
pubchem-query	Chemical Database	Query PubChem database for chemical structures, similar compounds (similarity search), and bioactivity data against protein targets.	Recommended
uniprot-query	Protein Database	Query UniProt database for protein sequences, comprehensive metadata (function, domains, diseases), and search by gene name, organism, or keywords.	Recommended
chembl-query	Bioactivity Database	Query ChEMBL database for bioactivity data on drug-like compounds by target, molecule, or disease indication.	Recommended
kegg-query	Pathway Database	Query KEGG database for drug information, pathway analysis, and disease-drug-target discovery.	Recommended
ppi-string-query	PPI Database	Query STRING database for protein-protein interactions with confidence scores for network analysis.	Recommended
biomedical-literature-search	Literature Search	Search PubMed and bioRxiv for biomedical research papers with titles, abstracts, and metadata.	Recommended

Utilities

Name	Category	Usage	Status
biomed-skill-router	Skill Discovery	Find the most suitable skill for a given biomedical task by analyzing user requests and matching against available skill capabilities.	Recommended
biomed-skill-creator	Skill Development	Create new biomedical skills or improve existing ones through an interactive validation process with intent capture, workflow design, and evaluation.	Recommended

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Notes

• Recommended skills contain examples/, references/, or evals/ directories with supporting documentation and test cases.
• Skills without a status are still being validated and may require additional documentation and testing.
• Skills are organized by primary category for easy navigation.
• Each skill includes a SKILL.md file with detailed workflow documentation, usage examples, and error handling guidelines.

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Categories Summary

Category	Count	Skills
Biochemistry & Drug Discovery	11	drug-candidate-discovery, drug-lead-analysis, target-based-lead-design, admet-prediction, retrosynthesis-planning, iupac-name-identification-biot5, molecule-biochemical-significance-query-biot5, text-based-molecule-editing, target-drug-report, disease-drug-intelligence, drug-drug-interaction-analysis
Protein Analysis & Engineering	13	protein-mutation-analysis, mutation-design-aav, mutation-design-gfp, functional-protein-design, protein-function-prediction, similar-protein-retrieval, structure-prediction-boltz-2, protein-structure-design-boltzgen, antibody-structure-prediction-tfold, antibody-design-iggm, binding-affinity-prediction-prodigy, protein-ligand-binding-analysis-plip, protein-subcellular-localization-prediction-biot5
Single-Cell Omics Data Analysis	13	single-cell-foundation-model-scrna-seq-geneformer, single-cell-foundation-model-scrna-seq-langcell, single-cell-foundation-model-scrna-seq-scgpt, spatial-transcriptomics-foundation-model-stofm, single-cell-scrna-seq-analysis-scanpy, single-cell-multi-omics-analysis-scvi, cellxgene-census-query, spatial-transcriptomics-spatial-data-io, single-cell-atac-seq-qc-processing, single-cell-atac-seq-peak-calling-annotaion, single-cell-proteomics-data-processing, single-cell-proteomics-peptide-identification, single-cell-multi-omics-data-harmonization
Data Retrieval & Knowledge	6	pubchem-query, uniprot-query, chembl-query, kegg-query, ppi-string-query, biomedical-literature-search
Utilities	2	biomed-skill-router, biomed-skill-creator

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Quick Reference by Use Case

I want to...	Use this skill
Design new drug candidates	drug-candidate-discovery, target-based-lead-design
Generate target drug reports	target-drug-report
Research disease-drug intelligence	disease-drug-intelligence
Analyze molecule properties	drug-lead-analysis, admet-prediction
Check drug-drug interactions	drug-drug-interaction-analysis
Find similar compounds	pubchem-query
Query protein database	uniprot-query
Analyze protein mutations	protein-mutation-analysis, mutation-design-aav, mutation-design-gfp
Predict protein structures	structure-prediction-boltz-2, antibody-structure-prediction-tfold
Design antibodies	antibody-design-iggm
Design proteins	protein-structure-design-boltzgen, functional-protein-design
Find similar proteins	similar-protein-retrieval
Predict binding affinity	binding-affinity-prediction-prodigy
Predict protein subcellular localization	protein-subcellular-localization-prediction-biot5
Analyze scRNA-seq data	single-cell-scrna-seq-analysis-scanpy, single-cell-multi-omics-analysis-scvi
Use single-cell foundation models	single-cell-foundation-model-scrna-seq-geneformer, single-cell-foundation-model-scrna-seq-scgpt, single-cell-foundation-model-scrna-seq-langcell
Analyze spatial transcriptomics	spatial-transcriptomics-foundation-model-stofm, spatial-transcriptomics-spatial-data-io
Query single-cell databases	cellxgene-census-query
Process ATAC-seq data	single-cell-atac-seq-qc-processing, single-cell-atac-seq-peak-calling-annotaion
Process proteomics MS data	single-cell-proteomics-data-processing, single-cell-proteomics-peptide-identification
Harmonize multi-omics data	single-cell-multi-omics-data-harmonization
Search biomedical literature	biomedical-literature-search
Get IUPAC name of a molecule	iupac-name-identification-biot5
Understand molecule's biochemical significance	molecule-biochemical-significance-query-biot5
Plan retrosynthesis routes	retrosynthesis-planning
Find the right skill	biomed-skill-router
Create a new skill	biomed-skill-creator