GitHub
pytdc
Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.
☆ 26View skill
tools computational chemistry AI Skills
Discover tools computational chemistry skills, compare source repositories and read the instructions for each workflow.
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GitHub
pdb-database
Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
☆ 26View skill
GitHub
gget
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads....
☆ 26View skill
GitHub
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
☆ 26View skill
GitHub
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
☆ 26View skill
GitHub
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use...
☆ 26View skill
GitHub
chembl-database
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
☆ 26View skill
GitHub
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
☆ 26View skill
GitHub
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
☆ 26View skill
GitHub
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used whe...
☆ 26View skill
GitHub
medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
☆ 26View skill
GitHub
matchms
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
☆ 26View skill
GitHub
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, paral...
☆ 26View skill
GitHub
pymatgen
Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.
☆ 26View skill
GitHub
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommenda...
☆ 25View skill
GitHub
clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, disc...
☆ 25View skill
GitHub
patent-reviewer
Expert system for reviewing utility patent applications against USPTO MPEP guidelines.
☆ 22View skill
GitHub
patent-application-creator
Complete end-to-end patent application creation from invention disclosure to USPTO-ready filing - prior art search, claims drafting, specification writing, diagrams, compliance checking
☆ 22View skill
GitHub
prd-v03-moat-definition
Assess competitor defensibility and define our own moat strategy during PRD v0.3 Commercial Model. Triggers on requests to analyze competitor moats, define our defensibility, assess switching costs, identify vu...
☆ 21View skill
GitHub
linear-solvers
Select and configure linear solvers for systems Ax=b in dense and sparse problems. Use when choosing direct vs iterative methods, diagnosing convergence issues, estimating conditioning, selecting preconditioner...
☆ 21View skill
GitHub
pm-prioritization
Feature prioritization frameworks - RICE scoring, ICE scoring, and Opportunity Solution Trees.
☆ 20View skill
GitHub
drama-workflow
Coordinate plot point dramatic function analysis process, manage text preprocessing, parallel analysis, result integration. Suitable for plot point and dramatic function analysis of long texts, scenarios requir...
☆ 20View skill
GitHub
research
Diagnose research quality and guide systematic query expansion. Use when starting research on any topic, when stuck in research, or when unsure if research is complete.
☆ 20View skill
GitHub
llm-council
Multi-model consensus using Karpathy LLM Council pattern for critical decisions
☆ 20View skill
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