Chemistry and Drug Discovery skills for Claude Code and Codex
Skills for chemistry and drug discovery: RDKit and Datamol molecule handling, Molfeat and DeepChem property prediction, medicinal chemistry filters, docking with DiffDock, GenMol and MolMIM generation on NVIDIA NIM, mass spectrometry with pyOpenMS and matchms, NMR processing, Cantera reactors, pharmacokinetic modeling and carbonate chemistry. They give an agent the cheminformatics procedures a lab trusts.
Highest-scoring chemistry skills in the October 22, 2026 snapshot: pkpd-modeling from K-Dense-AI/claude-scientific-skills (88/100) and differentiation-schemes from HeshamFS/materials-simulation-skills (82/100). Scores come from the Suede Skill Check.
- 28 listed skills
- 3 repositories
- 2 with full pages
6 from official publishers. 15 bundle scripts. 11 connect to an outside service. Listed in Science and Research (28).
All 28 chemistry skills
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| Skill | Repository | What it does |
|---|---|---|
| differentiation-schemes 82/100 · B | HeshamFS/materials-simulation-skills | Selects and applies numerical differentiation schemes for PDE and ODE discretization, including finite-difference stencils, central, upwind, compact and spectral methods. |
| pkpd-modeling 88/100 · B | K-Dense-AI/claude-scientific-skills | Supports pharmacokinetic and pharmacodynamic modelling and simulation, including non-compartmental analysis, population PK, exposure-response, bioequivalence, and dosing regimen evaluation from concentration-time data. |
| cantera 87/100 · B | K-Dense-AI/claude-scientific-skills | Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement… |
| datamol 79/100 · C | K-Dense-AI/claude-scientific-skills | Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing… |
| deepchem 81/100 · B | K-Dense-AI/claude-scientific-skills | Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked… |
| diffdock 89/100 · B | K-Dense-AI/claude-scientific-skills | Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose… |
| diffdock-nim 74/100 · C | NVIDIA/skills | Run DiffDock molecular docking via NVIDIA NIM to predict small-molecule binding poses against protein targets. Use for DiffDock, molecular docking… |
| drug-discovery-pipeline 68/100 · D | NVIDIA/skills | NOTE: molecule and target inputs and your NGC_API_KEY are transmitted to external NVIDIA-hosted API endpoints on every call. Use local NIM… |
| genmol-nim 77/100 · C | NVIDIA/skills | Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead… |
| marine-carbonate-chemistry 87/100 · B | K-Dense-AI/claude-scientific-skills | Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired… |
| matchms 93/100 · A | K-Dense-AI/claude-scientific-skills | Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral… |
| md-analysis-planner 73/100 · C | HeshamFS/materials-simulation-skills | Plan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle… |
| medchem 81/100 · B | K-Dense-AI/claude-scientific-skills | Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR… |
| molecular-dynamics 77/100 · C | K-Dense-AI/claude-scientific-skills | Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs… |
| molfeat 79/100 · C | K-Dense-AI/claude-scientific-skills | Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints… |
| molmim-nim 77/100 · C | NVIDIA/skills | Use this skill for MolMIM, NVIDIA's BioNeMo NIM microservice for small-molecule latent-space generation and optimization. Invoke for MolMIM… |
| nmrglue 87/100 · B | K-Dense-AI/claude-scientific-skills | Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration… |
| nvmolkit-usage 73/100 · C | NVIDIA/skills | Use when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches. |
| openfold3-nim 77/100 · C | NVIDIA/skills | Use this skill for OpenFold3, NVIDIA's BioNeMo NIM microservice for biomolecular structure prediction. Invoke whenever the user mentions OpenFold3… |
| pennylane 87/100 · B | K-Dense-AI/claude-scientific-skills | Builds and differentiates PennyLane quantum circuits, hybrid PyTorch or JAX models, molecular VQE and QAOA workflows. Use for variational quantum… |
| pyopenms 81/100 · B | K-Dense-AI/claude-scientific-skills | Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification… |
| pytdc 89/100 · B | K-Dense-AI/claude-scientific-skills | Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark… |
| qutip 87/100 · B | K-Dense-AI/claude-scientific-skills | Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space… |
| rdkit 81/100 · B | K-Dense-AI/claude-scientific-skills | Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search… |
| rowan 85/100 · B | K-Dense-AI/claude-scientific-skills | Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction… |
| tamarind 83/100 · B | K-Dense-AI/claude-scientific-skills | Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP… |
| tellurium 87/100 · B | K-Dense-AI/claude-scientific-skills | Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter… |
| torchdrug 87/100 · B | K-Dense-AI/claude-scientific-skills | Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation… |
How to choose chemistry skills
Start with RDKit or Datamol for parsing and descriptors, then add a task skill (docking, property prediction, generation) on top. The task skills assume clean SMILES or SDF input.
Hosted models (NVIDIA NIM, Rowan, Tamarind) send structures to an external API and read its key, shown under Before you install. Keep proprietary compounds off hosted services your agreements do not cover.
Treat predictions as candidates for experiment. medchem filters and docking scores rank molecules; your assays decide.
Related topics
Bioinformatics and Genomics 59Materials Science and Simulation 31Fine-Tuning and Model Training 127Machine Learning 29Physics and Quantum Computing 26
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