Computational Chemistry

Browse agent skills for molecular simulations, drug discovery, and chemical analysis

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25,177 results

healthcare-cdss-patterns

Sourceaffaan-m/ECC/docs/ja-JP/skills/healthcare-cdss-patterns/SKILL.md

Updated2026-05-17

臨床意思決定支援システム（CDSS）パターン、医学的推論、およびエビデンスベースの実装。

healthcare-cdss-patterns

Sourceaffaan-m/ECC/skills/healthcare-cdss-patterns/SKILL.md

Updated2026-08-12

Clinical Decision Support System (CDSS) development patterns. Drug interaction checking, dose validation, clinical scoring (NEWS2, qSOFA), alert severity classification, and integration into EMR workflows. Use when building clinical decision support — drug interaction checks, dose validation, clinical scoring, or alert severity.

evaluating-llms-harness

SourceNousResearch/hermes-agent/optional-skills/mlops/evaluation/evaluating-llms-harness/SKILL.md

Updated2026-09-18

lm-eval-harness: benchmark LLMs (MMLU, GSM8K, etc.).

faiss

SourceNousResearch/hermes-agent/optional-skills/mlops/faiss/SKILL.md

Updated2026-07-24

Fast vector similarity search at billion scale.

dspy

SourceNousResearch/hermes-agent/optional-skills/mlops/research/dspy/SKILL.md

Updated2026-06-04

DSPy: declarative LM programs, auto-optimize prompts, RAG.

drug-discovery

SourceNousResearch/hermes-agent/optional-skills/research/drug-discovery/SKILL.md

Updated2026-10-08

Drug discovery: ChEMBL search, drug-likeness, interactions.

fs-notebook-tabs

Sourcenexu-io/open-design/plugins/_official/examples/fs-notebook-tabs/SKILL.md

Updated2026-07-14

A computer-science capstone: an on-device ML keyboard that predicts next words privately — problem, method, evaluation, and defense answers. Built as a decision-grade coursework defense deck for professor, defense committee.

shader-dev

Sourcenexu-io/open-design/skills/shader-dev/SKILL.md

Updated2026-08-18

GLSL shader techniques for ray marching, fluid simulation, particle systems, and procedural generation. Useful for hero visuals and motion stills.

ruview-advanced-sensing

Sourceruvnet/RuView/plugins/ruview/skills/ruview-advanced-sensing/SKILL.md

Updated2026-05-11

Advanced RuView capabilities — RuvSense multistatic sensing (attention-weighted fusion, geometric diversity, persistent field model), cross-viewpoint fusion across multiple nodes, RF tomography (ISTA L1 solver, voxel grids), longitudinal biomechanics drift, pre-movement intention signals, adversarial signal detection, and multistatic mesh security hardening. Use for research-grade or multi-node deployments.

ruview-applications

Sourceruvnet/RuView/plugins/ruview/skills/ruview-applications/SKILL.md

Updated2026-05-11

Run RuView sensing applications — presence/occupancy, breathing & heart rate, activity & fall detection, 17-keypoint pose estimation (WiFlow), sleep monitoring & apnea screening, environment mapping, Mass Casualty Assessment (MAT), and the 3D point-cloud fusion demo. Use when someone wants to actually *do* something with a working RuView setup.

ruview-mmwave

Sourceruvnet/RuView/plugins/ruview/skills/ruview-mmwave/SKILL.md

Updated2026-05-11

Set up and run RuView mmWave / FMCW radar sensing — ESP32-C6 + Seeed MR60BHA2 (60 GHz, heart rate / breathing rate / presence) and HLK-LD2410 (24 GHz, presence + distance), plus mmWave↔WiFi-CSI sensor fusion (48-byte fused vitals, MR60BHA2/LD2410 auto-detect, v0.5.0+). Use when the deployment includes a millimetre-wave radar alongside or instead of WiFi CSI.

vector-search

Sourceruvnet/ruflo/plugins/ruflo-agentdb/skills/vector-search/SKILL.md

Updated2026-10-11

Vector search via embeddings_* (large-scale HNSW) and ruvllm_hnsw_* (WASM router for ≤11 hot patterns), with RaBitQ 1-bit quantization for 32× memory reduction

cli-anything-unimol-tools

SourceHKUDS/CLI-Anything/skills/cli-anything-unimol-tools/SKILL.md

Updated2026-04-18

Interactive CLI for Uni-Mol molecular property prediction training and inference workflows.

cli-anything-unimol-tools

SourceHKUDS/CLI-Anything/unimol_tools/agent-harness/cli_anything/unimol_tools/SKILL.md

Updated2026-04-18

Interactive CLI for Uni-Mol molecular property prediction training and inference workflows.

adaptyv

SourceK-Dense-AI/scientific-agent-skills/skills/adaptyv/SKILL.md

Updated2026-10-01

Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies to Adaptyv Foundry, its target catalog, binding screening and affinity assays, thermostability, expression, fluorescence, epitope binning, and enzyme activity workflows, including code using adaptyv or FoundryClient.

cantera

SourceK-Dense-AI/scientific-agent-skills/skills/cantera/SKILL.md

Updated2026-10-01

Runs Cantera homogeneous chemical reactors and evaluates ignition delay with mechanism provenance, conservation checks, and numerical refinement. Use for combustion kinetics, closed adiabatic ideal-gas constant-volume or constant-pressure ignition, temperature histories, or mechanism-specific ignition-delay comparisons.

cellprofiler

SourceK-Dense-AI/scientific-agent-skills/skills/cellprofiler/SKILL.md

Updated2026-10-01

Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence assays.

cirq

SourceK-Dense-AI/scientific-agent-skills/skills/cirq/SKILL.md

Updated2026-10-01

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.

datamol

SourceK-Dense-AI/scientific-agent-skills/skills/datamol/SKILL.md

Updated2026-10-01

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.

deepchem

SourceK-Dense-AI/scientific-agent-skills/skills/deepchem/SKILL.md

Updated2026-10-01

Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder transfer. Used for ADMET, toxicity, solubility and chemistry ML when DeepChem data/model contracts and scientific validation are needed.

depmap

SourceK-Dense-AI/scientific-agent-skills/skills/depmap/SKILL.md

Updated2026-10-01

Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity. Supports cancer-selective dependency, co-essentiality, and candidate synthetic-lethality analyses with release-aware identifiers and statistical checks.

diffdock

SourceK-Dense-AI/scientific-agent-skills/skills/diffdock/SKILL.md

Updated2026-10-01

Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.

fluidsim

SourceK-Dense-AI/scientific-agent-skills/skills/fluidsim/SKILL.md

Updated2026-10-01

Plans, configures, inspects, restarts, and analyzes bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection, parameter review, FFT/MPI setup, output diagnostics, or restart compatibility.

mageck

SourceK-Dense-AI/scientific-agent-skills/skills/mageck/SKILL.md

Updated2026-10-01

Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect sizes and FDR. Use for new knockout, CRISPRi, or CRISPRa screen analysis, enrichment or depletion contrasts, and MAGeCK count/test workflows; existing public dependency-score lookup belongs to DepMap.

medchem

SourceK-Dense-AI/scientific-agent-skills/skills/medchem/SKILL.md

Updated2026-10-01

Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.

molecular-dynamics

SourceK-Dense-AI/scientific-agent-skills/skills/molecular-dynamics/SKILL.md

Updated2026-10-01

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis. Sets up protein/small molecule systems, defines force fields, runs energy minimization and production MD, and analyzes trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.

molfeat

SourceK-Dense-AI/scientific-agent-skills/skills/molfeat/SKILL.md

Updated2026-10-01

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML. Covers ECFP/MACCS fingerprints, RDKit descriptors, pharmacophores, pretrained embeddings, configuration persistence, and molecule-to-label alignment.

nmrglue

SourceK-Dense-AI/scientific-agent-skills/skills/nmrglue/SKILL.md

Updated2026-10-01

Processes calibrated one-dimensional complex NMR free-induction decays with nmrglue into phased spectra, peak candidates, and signed integration regions. Use for raw 1D NMR processing, ppm-axis verification, apodization, Fourier transformation, manual phasing, baseline correction, or reproducible spectral integration.

openpiv

SourceK-Dense-AI/scientific-agent-skills/skills/openpiv/SKILL.md

Updated2026-10-01

Performs Particle Image Velocimetry (PIV) analysis with OpenPIV. Use when extracting velocity fields from PIV image pairs, analyzing fluid dynamics or flow visualization experiments, cross-correlating interrogation windows, validating and replacing spurious PIV vectors, or computing vorticity, strain rate, and turbulence statistics from measured velocity fields.

pkpd-modeling

SourceK-Dense-AI/scientific-agent-skills/skills/pkpd-modeling/SKILL.md

Updated2026-10-01

Pharmacokinetic and pharmacodynamic modelling and simulation - non-compartmental analysis, compartmental and population PK, PK/PD and exposure-response, TMDD, PBPK orientation, bioequivalence, allometric scaling and first-in-human dose, drug interaction prediction, and Bayesian therapeutic drug monitoring. Use when analysing concentration-time data, deriving exposure metrics, fitting PK or PD models, or evaluating dosing regimens. Triggers include "pharmacokinetics", "pharmacodynamics", "PK/PD", "NCA", "non-compartmental", "AUC", "Cmax", "lambda z", "half-life", "clearance", "volume of distribution", "compartmental model", "population PK", "popPK", "NONMEM", "nlmixr2", "Pharmpy", "Monolix", "exposure-response", "Emax", "EC50", "indirect response", "effect compartment", "TMDD", "PBPK", "bioequivalence", "RSABE", "ABEL", "allometric scaling", "first-in-human", "MABEL", "drug-drug interaction", "DDI", "ICH M12", "concentration-QTc", "therapeutic drug monitoring", "MIPD", and "dosing regimen".

primer-design

SourceK-Dense-AI/scientific-agent-skills/skills/primer-design/SKILL.md

Updated2026-10-01

Designs and audits PCR and RT-qPCR primers with Primer3, explicit thermodynamic conditions, reference-based off-target amplification searches, and traceable sequence coordinates. Use for designing primer pairs, checking existing primers, exon-junction or isoform-specific assays, variant masking, cloning tails, multiplex compatibility, and interpreting Primer-BLAST results. Includes bounded local in-silico PCR and BLAST screening; distinguishes computational candidates from experimentally validated assays.

pycalphad

SourceK-Dense-AI/scientific-agent-skills/skills/pycalphad/SKILL.md

Updated2026-10-01

Computes finite-temperature CALPHAD equilibria, phase fractions, and phase compositions from thermodynamic TDB databases using pycalphad. Use for alloy phase stability, equilibrium temperature sweeps, tie lines, lever-rule checks, or reproducible phase-fraction calculations with explicit components and mole-fraction conditions.

qutip

SourceK-Dense-AI/scientific-agent-skills/skills/qutip/SKILL.md

Updated2026-10-01

Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.

rdkit

SourceK-Dense-AI/scientific-agent-skills/skills/rdkit/SKILL.md

Updated2026-10-01

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

rowan

SourceK-Dense-AI/scientific-agent-skills/skills/rowan/SKILL.md

Updated2026-10-01

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU infrastructure.

tellurium

SourceK-Dense-AI/scientific-agent-skills/skills/tellurium/SKILL.md

Updated2026-10-01

Simulates biochemical kinetic models from SBML or Antimony with Tellurium and libRoadRunner, checks model units, compares deterministic parameter perturbations, and exports and replays SBML plus SED-ML COMBINE archives. Use for reaction-network time courses, kinetic parameters, concentration dynamics and reproducible simulation experiments; steady-state constraint-based metabolic flux analysis belongs to cobrapy.

use-vishot-with-capacitor

Sourcemoeru-ai/airi/.agents/skills/use-vishot-with-capacitor/SKILL.md

Updated2026-08-04

Capture deterministic Capacitor application screens with Vishot. Use when the selected Vishot target is a Capacitor app and Codex must capture its locally served WebView at mobile dimensions or distinguish WebView evidence from native-shell evidence.

use-vishot-with-electron

Sourcemoeru-ai/airi/.agents/skills/use-vishot-with-electron/SKILL.md

Updated2026-08-05

Capture deterministic Electron windows with Vishot. Use when the selected Vishot target is an Electron application and Codex must identify, prepare, and capture one or more renderer windows without relying on window creation order or agent-browser.

pixijs-scene-particle-container

Sourcepixijs/pixijs/skills/pixijs-scene-particle-container/SKILL.md

Updated2026-09-16

Use this skill when rendering thousands of lightweight sprites in PixiJS v8. Covers ParticleContainer with Particle instances, addParticle/removeParticle, particleChildren array, dynamicProperties (vertex, position, rotation, uvs, color), boundsArea, roundPixels, update, inherited alpha/tint/blendMode from ancestors. Triggers on: ParticleContainer, Particle, IParticle, addParticle, particleChildren, dynamicProperties, boundsArea, particle effects, particle alpha, particle tint, fade particles, constructor options, ParticleContainerOptions, ParticleOptions.

math-olympiad

Sourceanthropics/claude-plugins-official/plugins/math-olympiad/skills/math-olympiad/SKILL.md

Updated2026-03-30

Solve competition math problems (IMO, Putnam, USAMO, AIME) with adversarial verification that catches the errors self-verification misses. Activates when asked to 'solve this IMO problem', 'prove this olympiad inequality', 'verify this competition proof', 'find a counterexample', 'is this proof correct', or for any problem with 'IMO', 'Putnam', 'USAMO', 'olympiad', or 'competition math' in it. Uses pure reasoning (no tools) — then a fresh-context adversarial verifier attacks the proof using specific failure patterns, not generic 'check logic'. Outputs calibrated confidence — will say 'no confident solution' rather than bluff. If LaTeX is available, produces a clean PDF after verification passes.

digital-forensics

Sourcezhaoxuya520/reverse-skill/skills/digital-forensics/SKILL.md

Updated2026-08-08

Use for authorized digital forensics including memory dumps, disk timelines, PCAP investigation, artifact triage, and IR evidence preservation.

Skill content language: Chinese

llm-security

Sourcezhaoxuya520/reverse-skill/skills/llm-security/SKILL.md

Updated2026-08-12

Use for authorized security assessment of LLM applications and AI agents, including prompt injection, tool abuse, RAG exposure, memory poisoning, and model supply-chain risks.

Skill content language: Chinese

malware-analysis

Sourcezhaoxuya520/reverse-skill/skills/malware-analysis/SKILL.md

Updated2026-08-12

Use when analyzing suspected malware through static, dynamic, and behavioral techniques, including IOC extraction, YARA or Sigma rules, sandboxing, and anti-analysis behavior.

Skill content language: Chinese

ot-ics

Sourcezhaoxuya520/reverse-skill/skills/ot-ics/SKILL.md

Updated2026-08-08

Use for authorized OT/ICS security assessment covering Purdue model zoning, PLC/SCADA exposure, industrial protocol discovery, and safe passive-first evaluation.

Skill content language: Chinese

radio-sdr

Sourcezhaoxuya520/reverse-skill/skills/radio-sdr/SKILL.md

Updated2026-08-08

Use for authorized RF/SDR security research including signal identification, replay feasibility study in shielded labs, and wireless protocol analysis outside classic Wi-Fi.

Skill content language: Mixed languages

embedding-strategies

Sourcewshobson/agents/plugins/llm-application-dev/skills/embedding-strategies/SKILL.md

Updated2026-05-22

Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.

analyzing-campaign-attribution-evidence

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/analyzing-campaign-attribution-evidence/SKILL.md

Updated2026-08-02

Systematically evaluate cyber-campaign evidence to attribute an operation to a threat actor, using the Diamond Model and Analysis of Competing Hypotheses (ACH) to weigh infrastructure overlaps, TTP consistency, malware code similarity, and timing/language artifacts into confidence-weighted attribution assessments. Use when an incident investigation needs a defensible attribution confidence level.

assessing-vector-and-embedding-weaknesses

Sourcemukul975/Anthropic-Cybersecurity-Skills/skills/assessing-vector-and-embedding-weaknesses/SKILL.md

Updated2026-08-02

Test RAG vector stores (Pinecone, Qdrant, Weaviate, Chroma, pgvector, FAISS) for embedding inversion, cross-tenant data leakage, and data poisoning per OWASP LLM08:2025. Use when performing an authorized security assessment of a RAG pipeline's retrieval layer or auditing multi-tenant vector-store isolation.