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Molecular modeling and reactions.

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computational-chemistry

2K

tooluniverse-drug-target-validation

Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimensions (disambiguation, disease association, druggability, chemical matter, clinical precedent, safety, pathway context, validation evidence, structural insights, validation roadmap) using 60+ ToolUniverse tools. Produces a quantitative Target Validation Score (0-100) with GO/NO-GO recommendation. Use when users ask about target validation, druggability assessment, target prioritization, or "is X a good drug target for Y?"

FreedomIntelligence

research

computational-chemistry

2K

tooluniverse-immunotherapy-response-prediction

Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and optional biomarkers (TMB, PD-L1, MSI status), performs systematic analysis across 11 phases covering TMB classification, neoantigen burden estimation, MSI/MMR assessment, PD-L1 evaluation, immune microenvironment profiling, mutation-based resistance/sensitivity prediction, clinical evidence retrieval, and multi-biomarker score integration. Generates a quantitative ICI Response Score (0-100), response likelihood tier, specific ICI drug recommendations with evidence, resistance risk factors, and a monitoring plan. Use when oncologists ask about immunotherapy eligibility, checkpoint inhibitor selection, or biomarker-guided ICI treatment decisions.

FreedomIntelligence

research

computational-chemistry

2K

tooluniverse-infectious-disease

Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.

FreedomIntelligence

research

computational-chemistry

2K

tooluniverse-pharmacovigilance

Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug safety, adverse events, post-market surveillance, or risk-benefit assessment.

FreedomIntelligence

research

computational-chemistry

2K

tooluniverse-precision-oncology

Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.

FreedomIntelligence

research

computational-chemistry

2K

tooluniverse-rare-disease-diagnosis

Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.

FreedomIntelligence

research

computational-chemistry

1.8K

judgment-day

Parallel adversarial review protocol that launches two independent blind judge sub-agents simultaneously to review the same target, synthesizes their findings, applies fixes, and re-judges until both pass or escalates after 2 iterations. Trigger: When user says "judgment day", "judgment-day", "review adversarial", "dual review", "doble review", "juzgar", "que lo juzguen".

Gentleman-Programming

research

computational-chemistry

1.8K

investigate

Chain-loaded investigation. 5-phase Iron Law methodology with root cause gate.

catlog22

research

computational-chemistry

1.6K

judgment-day

Parallel adversarial review protocol that launches two independent blind judge sub-agents simultaneously to review the same target, synthesizes their findings, applies fixes, and re-judges until both pass or escalates after 2 iterations. Trigger: When user says "judgment day", "judgment-day", "review adversarial", "dual review", "doble review", "juzgar", "que lo juzguen".

Gentleman-Programming

research

computational-chemistry

1.3K

chembl-database

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

foryourhealth111-pixel

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computational-chemistry

1.3K

cirq

Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.

foryourhealth111-pixel

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computational-chemistry

1.3K

datamol

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

foryourhealth111-pixel

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computational-chemistry

1.3K

deepchem

Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

foryourhealth111-pixel

research

computational-chemistry

1.3K

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 when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.

foryourhealth111-pixel

research

computational-chemistry

1.3K

fda-database

Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

foryourhealth111-pixel

research

computational-chemistry

1.3K

histolab

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

foryourhealth111-pixel

research

computational-chemistry

1.3K

matchms

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

foryourhealth111-pixel

research

computational-chemistry

1.3K

medchem

Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

foryourhealth111-pixel

research

computational-chemistry

1.3K

pubchem-database

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

foryourhealth111-pixel

research

computational-chemistry

1.3K

qiskit

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.

foryourhealth111-pixel

research

computational-chemistry

1.3K

qutip

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

foryourhealth111-pixel

research

computational-chemistry

1.3K

rowan

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2). Use when tasks involve quantum chemistry calculations, molecular property prediction, DFT or semiempirical methods, neural network potentials (AIMNet2), protein-ligand binding predictions, or automated computational chemistry pipelines. Provides cloud compute resources with no local setup required.

foryourhealth111-pixel

research

computational-chemistry

1.3K

stable-baselines3

Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.

foryourhealth111-pixel

research

computational-chemistry

1.3K

torch-geometric

Compatibility alias for the underscore PyG skill name. Delegate to the canonical local `torch-geometric` payload while preserving route compatibility.

foryourhealth111-pixel

research

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