GitHub
imc-tuning-rules
Calculate PI/PID controller gains using Internal Model Control (IMC) tuning rules for first-order systems.
☆ 283View 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
rdkit
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 w...
☆ 283View 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.
☆ 283View skill
GitHub
attack-tree-construction
Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
☆ 279View skill
GitHub
pycse
Python computations in science and engineering (pycse) - helps with scientific computing tasks including nonlinear regression, uncertainty quantification, design of experiments (DOE), Latin hypercube sampling,...
☆ 272View skill
GitHub
weather-pollen
Weather and pollen reports for any location using free APIs. Get current conditions, forecasts, and pollen data.
☆ 229View skill
GitHub
gemini-deep-research
Perform complex, long-running research tasks using Gemini Deep Research Agent. Use when asked to research topics requiring multi-source synthesis, competitive analysis, market research, or comprehensive technic...
☆ 229View skill
GitHub
nextflow-development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core,...
☆ 210View skill
GitHub
clinical-trial-protocol-skill
Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical stu...
☆ 210View skill
GitHub
instrument-data-to-allotrope
Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS sys...
☆ 210View skill
GitHub
swot-pestle-analysis
Strategic environmental analysis using SWOT, PESTLE, and Porter's Five Forces. Creates structured assessments with Mermaid visualizations for competitive positioning and strategic planning.
☆ 208View skill
GitHub
pdbe-api
Query the PDBe (Protein Data Bank in Europe) REST API and Solr search API from within Coot to access structure metadata, validation data, revision history, and search capabilities
☆ 155View skill
GitHub
coot-rdkit
RDKit molecular manipulation and visualization within Coot's Python environment. Use when working with Coot and need to (1) Create RDKit molecules from Coot monomers, (2) Modify molecular structures (e.g., atom...
☆ 154View skill
GitHub
coot-correlations
Using Density-Fit Correlations in Coot
☆ 154View skill
GitHub
coot-refinement
Best practices for protein structure refinement and validation in Coot. Use when performing (1) Residue refinement operations, (2) Model building and fitting, (3) Rotamer fixing, (4) Scripted/automated refineme...
☆ 154View skill
GitHub
coot-validation
Comprehensive structure validation combining model-to-map analysis and unmodeled density detection
☆ 154View skill
GitHub
claude-scientific-skills
Comprehensive collection of 128+ ready-to-use scientific skills for Claude enabling research across biology, chemistry, medicine, genomics, and advanced analysis domains.
☆ 129View skill
GitHub
packmol
This skill should be used when the user asks to "create a packmol input", "pack molecules with packmol", "solvate a protein", "build an initial configuration", "setup molecular dynamics", or discusses molecular...
☆ 124View skill
GitHub
attack-tree-construction
Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.
☆ 124View skill
GitHub
reasoning-inductive
Extract patterns and generalizations from multiple observations. Use when detecting recurring themes, building predictive rules, or identifying systemic behaviors from accumulated data. Produces validated patte...
☆ 123View skill
GitHub
reasoningbank-adaptive-learning-with-agentdb
Implement ReasoningBank adaptive learning with AgentDB for trajectory tracking, verdict judgment, memory distillation, and pattern recognition to build self-learning agents that improve decision-making through...
☆ 123View skill
GitHub
build-diagnostics
When given a blocker:
☆ 123View skill
GitHub
firstprinciples
First principles analysis. USE WHEN first principles, fundamental, root cause, decompose. SkillSearch('firstprinciples') for docs.
☆ 99View skill
GitHub
competitive-research
Research competitors, analyze market positioning, identify differentiators, and understand competitive landscape to inform product strategy and positioning. Use when researching competitors, analyzing features,...
☆ 95View skill
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