279 tagged cheminformatics, measured the same way as everything else here.
Browse within: bioinformatics 184chemistry 63calphad 57computational-chemistry 57computational-biology 56agent-plugins 37drug-discovery 35bioactivity 32chembl 32compounds 32cyanheads 32engineering 32ip 32lifescience 32
Skill Claude CodeCodex
Patsnap Patent Research MCP for AI agents. Performs novelty searches, invention freedom-to-operate reviews, and design-patent FTO reviews from technical text, claims, disclosures, or product images. Use for defined novelty and infringement-risk research workflows, including asynchronous task retrieval; do not use it…
Skill Claude CodeCodex
Patsnap Pharma Intelligence MCP for AI agents. Search clinical trials, drugs, patents, papers, deals, FDA labels and more via 28 specialized tools.
Skill Claude CodeCodex
Patsnap TRIZ Concept Solution Engine MCP for AI agents. Generates innovation or product cost-reduction concepts through asynchronous TRIZ and TRIZ/DFMA workflows. Use for engineering problem solving, concept alternatives, cost-reduction analysis, task-progress retrieval, and selected-solution details.
Laboratoire-de-Chemoinformatique/SynPlanner
Skill Claude CodeCodex
Plan retrosynthetic routes, curate reaction data, extract reaction rules, train retrosynthesis policy and value networks, and analyse synthetic routes with the installed SynPlanner package. SynPlanner is built on chython (chython-synplan, formerly CGRtools), not RDKit. Use when the user imports synplan., asks for a…
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all required tools are installed, executable, meet version requirements (e.g., samtools ≥1.
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when when you have aligned ChIP-Seq reads (single-end BED or paired-end BEDPE format) and need to identify enriched genomic regions by comparing ChIP signal against control background, with the ability to customize fragment length estimation, local bias calculation, and peak score thresholds.
HolobiomicsLab/asb-skill-collections
Skill Claude CodeCodex
Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually occupied by proteins in your cell type or condition.
K-Dense-AI/drug-discovery-agent-skills
Skill Claude CodeCodex
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then…
K-Dense-AI/drug-discovery-agent-skills
Skill Claude CodeCodex
Molecular featurization hub with one consistent interface over 100+ featurizers. Fingerprints (ECFP/Morgan, MACCS, atom pair, topological torsion, Avalon, RDKit, ERG), RDKit and Mordred descriptor sets, pharmacophore and 3D shape descriptors, scaffold keys, and pretrained embeddings (ChemBERTa, ChemGPT, MolT5, GIN…
K-Dense-AI/drug-discovery-agent-skills
Skill Claude CodeCodex
Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design…
Skill Claude CodeCodex
Scaffold a new MCP tool definition. Use when the user asks to add a tool, create a new tool, or implement a new capability for the server.
Skill Claude CodeCodex
Canonical reference for the unified Context object passed to every tool and resource handler in @cyanheads/mcp-ts-core. Covers the full interface, its RequestContext base, all sub-APIs (ctx.log, ctx.state, ctx.requestInput, ctx.inputs, ctx.enrich, ctx.content), and when to use each.
Skill Claude CodeCodex
Design the tool surface, resources, and service layer for a new MCP server. Use when starting a new server, planning a major feature expansion, or when the user describes a domain/API they want to expose via MCP. Produces a design doc at docs/design.md that drives implementation.
Skill Claude CodeCodex
Bench-chemistry flavor & aroma analysis from chemical structure. Use when working on food/beverage flavor formulation, ingredient substitution, or molecular taste/aroma questions: predict a molecule's taste (6 heads) and aroma (24 heads); analyze a whole formulation "before you pour" (blended note-profile…
Skill Claude CodeCodex
Use at the start of any computational chemistry task to structure thinking, map available tools, and generate concrete hypotheses. Covers molecule evaluation, hypothesis building, reaction assessment, and pipeline design. Flexible guide — adapt depth to problem complexity.
Skill Claude CodeCodex
Use when performing protein-ligand docking, virtual screening, or structure-based drug design. Covers receptor preparation (protonation, pocket definition), AutoDock Vina/Gnina docking engines, high-throughput virtual screening pipelines, pose analysis with interaction fingerprints, and ensemble docking for protein…
Skill Claude CodeCodex
Use when working with PepFlex for in silico peptide screening and evolutionary optimization. Handles peptide population management, mutation, crossover, custom evaluation pipelines, and multi-round evolutionary simulation.
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers quantitative post-processing of atomistic molecular dynamics trajectories: loading and preprocessing trajectories from LAMMPS, GROMACS, or ASE; computing structural observables (RDF, coordination numbers, angular distributions, bond orientational order, common-neighbor analysis, centrosymmetry…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers selection, validation, and deployment of interatomic force fields for molecular dynamics: the physical basis and transferability limits of every major functional form (EAM, MEAM, Tersoff, Stillinger-Weber, Buckingham, COMB, ReaxFF, AMBER, CHARMM, OPLS, GROMOS, and ML potentials); parameter-file…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers reactive molecular dynamics (reactive MD) using LAMMPS with the ReaxFF and COMB force fields: force-field selection and parameter provenance, charge equilibration (QEq) setup and diagnostics, timestep and thermostat selection for reactive systems, thermal protocols for reaction sampling, reaction…
Skill Claude CodeCodex
Scaffold a new MCP tool definition. Use when the user asks to add a tool, create a new tool, or implement a new capability for the server.
Skill Claude CodeCodex
MCP definition linter rules reference. Use when bun run lint:mcp or bun run devcheck reports a lint error or warning (format-parity, schema-is-object, name-format, server-json-, etc.) and you need to understand the rule, its severity, and how to fix it. Every rule ID the linter emits has an entry in this doc.
Skill Claude CodeCodex
Design the tool surface, resources, and service layer for a new MCP server. Use when starting a new server, planning a major feature expansion, or when the user describes a domain/API they want to expose via MCP. Produces a design doc at docs/design.md that drives implementation.