← all publishers

K-Dense AI

@k-dense-ai source repo

Report this profile Claim this profile

• 344 skills
• 0 followers
• 30k repo stars
• 2 weeks ago last updated

1. ▌
   Citation Management 3 · k-dense-ai bundle

   Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
   30.2k repo stars
2. ▌
   Esm 2 · k-dense-ai bundle

   Protein language models through the EvolutionaryScale `esm` Python SDK. Generate and embed sequences with ESM3 (multimodal sequence, structure and function prompting), extract per-residue and mean-pooled embeddings with ESM C, fold sequences with ESMFold2, and run inference locally or against the Forge and Biohub hosted clients. Use this skill for protein representation learning, variant effect and mutational scanning from likelihoods, sequence generation and inpainting, structure prediction from sequence alone, and embedding features for downstream models. Also trigger on esm, ESM3, ESMC, ESM Cambrian, ESMFold2, `from esm.models`, ESMProtein, GenerationConfig, forge.evolutionaryscale.ai, biohub.ai, or ESM_API_KEY.
   30.2k repo stars
3. ▌
   Pytdc 2 · k-dense-ai bundle

   Use Therapeutics Data Commons through the PyTDC Python package for registry discovery, approved dataset access, task-aware splits (scaffold, cold-start, temporal, combination), evaluator metrics, benchmark groups, and bounded molecular-oracle workflows. Use this skill to find which TDC datasets exist for a therapeutic task, load them with a split that does not leak, score predictions with the task's own official metric rather than a generic one, and run benchmark groups reproducibly. Also trigger on PyTDC, Therapeutics Data Commons, tdc.single_pred, tdc.multi_pred, ADMET Benchmark Group, scaffold split, get_split, or molecular oracles such as GSK3B, JNK3 and DRD2.
   30.2k repo stars
4. ▌
   Rdkit 2 · k-dense-ai bundle

   Cheminformatics toolkit for fine-grained molecular control. Parse and write SMILES, SDF, MOL and InChI; compute descriptors (MW, LogP, TPSA, QED, Bertz); build fingerprints (Morgan/ECFP, RDKit, MACCS, atom pair, torsion) and score Tanimoto, Dice or cosine similarity; run SMARTS substructure search and reaction SMARTS; generate 2D depictions and ETKDG 3D conformers; extract Murcko scaffolds and canonical hashes; control sanitization and stereochemistry directly. Also trigger on rdkit, Chem.MolFromSmiles, rdFingerprintGenerator, SDMolSupplier, SMARTS query, ETKDG, or FilterCatalog. For standard workflows with a simpler interface use the datamol skill, which wraps RDKit; use rdkit for advanced control, custom sanitization, and specialized algorithms.
   30.2k repo stars
5. ▌
   Rowan 2 · k-dense-ai bundle

   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.
   30.2k repo stars
6. ▌
   Depmap 2 · k-dense-ai bundle

   Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), RNAi DEMETER2 scores, PRISM compound sensitivity, and gene effect profiles across the cell-line panel. Use for identifying cancer-selective vulnerabilities, separating pan-essential genes from selective ones, finding synthetic lethal interactions, correlating dependency with mutation, expression and copy number, and validating oncology drug targets. Also trigger on DepMap, Chronos gene effect, CRISPRGeneEffect.csv, DEMETER2, PRISM repurposing, co-essentiality, pan-essential, or ACH- cell line identifiers.
   30.2k repo stars
7. ▌
   Adaptyv 2 · k-dense-ai bundle

   How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.
   30.2k repo stars
8. ▌
   Datamol 2 · k-dense-ai bundle

   Pythonic wrapper around RDKit with a simplified interface and sensible defaults. Preferred for standard drug discovery work — SMILES/SELFIES/InChI conversion, molecule standardization and sanitization, descriptors, ECFP and other fingerprints, Tanimoto distance matrices, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds and scaffold splits, BRICS/RECAP fragmentation, 3D conformer generation, SDF/CSV/Excel and cloud I/O, and parallel processing via n_jobs. Returns native rdkit.Chem.Mol objects, so it composes with RDKit throughout. Also trigger on datamol, `import datamol as dm`, dm.to_mol, dm.standardize_mol, dm.cluster_mols, or dm.pick_diverse. For advanced control or custom parameters, use the rdkit skill directly.
   30.2k repo stars
9. ▌
   Medchem 2 · k-dense-ai bundle

   Medicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski rule of five, Veber, Oprea, CNS, lead-like, rule of three), structural alert catalogs (PAINS a/b/c, NIBR screening-deck severity, Brenk, BMS, Glaxo, Dundee, ChEMBL common alerts), ZINC-15 percentile complexity metrics (Bertz, SAscore, QED, Whitlock, Barone), chemical-group detection, Lilly demerits, and the medchem query language (MATCHRULE, HASALERT, HASPROP, HASGROUP) for filtering a library at scale. Also trigger on medchem, `import medchem as mc`, RuleFilters, NIBRFilters, CommonAlertsFilters, NamedCatalogs, QueryFilter, PAINS filtering, or structural alerts.
   30.2k repo stars
10. ▌
    Molfeat 2 · k-dense-ai bundle

    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, Graphormer) through a common transformer API with caching and parallelism. Use this skill to convert SMILES into model-ready feature matrices for QSAR, virtual screening, and molecular ML, and to choose between featurizer families. Also trigger on molfeat, MoleculeTransformer, FPVecTransformer, PretrainedHFTransformer, molfeat model store, or featurizer selection.
    30.2k repo stars
11. ▌
    Primekg 2 · k-dense-ai bundle

    Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy. Use this skill to search entities by name, pull direct neighbours and their evidence types, summarise the local network around a disease, and find direct or two-hop drug-disease connections for repurposing hypotheses. Also trigger on PrimeKG, kg.csv, Harvard Dataverse knowledge graph, disease_protein, drug_protein, indication and contraindication edges, or network pharmacology over a biomedical knowledge graph.
    30.2k repo stars
12. ▌
    Deepchem 2 · k-dense-ai bundle

    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 ready-made ADMET numbers without training a model use admet-prediction; for benchmark datasets and task-aware splits use pytdc.
    30.2k repo stars
13. ▌
    Diffdock 2 · k-dense-ai bundle

    DiffDock and DiffDock-L diffusion-based molecular docking. Use for blind protein-small-molecule pose prediction from a PDB file or sequence plus SMILES/SDF/MOL2, batch docking over a CSV of complexes, virtual screening triage, sampling multiple poses per complex, and reading the confidence score correctly. Also trigger on DiffDock, DiffDock-L, inference.py, confidence_model, samples_per_complex, ESM embedding preparation for docking, or blind docking without a defined box. Not for binding affinity prediction — the confidence score ranks pose plausibility, not potency.
    30.2k repo stars
14. ▌
    Tamarind 2 · k-dense-ai bundle

    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 (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.
    30.2k repo stars
15. ▌
    Ncats Arax 2 · k-dense-ai bundle

    Queries the NCATS Translator ARAX production API for bounded, typed, provenance-rich one-hop and endpoint-pinned two-hop biomedical knowledge-graph relationships. Use for Biolink-constrained RTX-KG2 lookup, explicit selected-provider ARAX federation, separate entity normalization, qualifier-aware graph traversal, and inspection of TRAPI edge bindings, publications, and knowledge-source provenance. Do not use for inference, ranking, open-ended pathfinding, clinical guidance, or sensitive queries.
    30.2k repo stars
16. ▌
    Glycoengineering 2 · k-dense-ai bundle

    Analyze and engineer protein glycosylation. Scan sequences for canonical N-glycosylation sequons (N-X-S/T with X not proline, including overlapping sites), predict O-GalNAc hotspots, read glycan notation, and reach the curated external tooling (NetNGlyc, NetOGlyc, GlycoShield, GlycoWorkbench, GlyTouCan, GlyConnect). Use this skill for therapeutic antibody glycoengineering and afucosylation for ADCC, Fc glycan control, glycan shielding in vaccine immunogen design, sequon removal or insertion, and half-life engineering through sialylation. Also trigger on N-glycosylation, sequon, NXS/NXT, O-glycosylation, glycoform heterogeneity, afucosylation, high-mannose, GlyTouCan, or WURCS.
    30.2k repo stars
17. ▌
    Molecular Dynamics 2 · k-dense-ai bundle

    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 analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free energy surfaces. Use this skill for protein stability under mutation, ligand binding-mode and residence-time questions, conformational sampling, membrane proteins, and disordered ensembles. Also trigger on OpenMM, MDAnalysis, mdtraj, Simulation.step, LangevinMiddleIntegrator, PDBFixer, DCD or XTC trajectory, RMSD analysis, or production MD.
    30.2k repo stars
18. ▌
    DOCX 2 · k-dense-ai bundle

    Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx or .dotx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation.
    30.2k repo stars
19. ▌
    PPTX 2 · k-dense-ai bundle

    Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates (.potx), layouts, speaker notes, or comments. Trigger whenever the user mentions "deck," "slides," "presentation," or references a .pptx or .potx filename, regardless of what they plan to do with the content afterward. If a .pptx or .potx file needs to be opened, created, or touched, use this skill.
    30.2k repo stars
20. ▌
    Statistical Analysis 2 · k-dense-ai bundle

    Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Use whenever a user wants to compare groups, test a hypothesis, analyze experimental or survey data, check statistical assumptions, compute required sample sizes, or write up results - even if they never name a specific test. Covers t-tests, ANOVA, chi-square, correlation, regression, non-parametric and Bayesian methods. For low-level model APIs, see the statsmodels and pymc skills.
    30.2k repo stars
21. ▌
    Scientific Critical Thinking 2 · k-dense-ai bundle

    Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
    30.2k repo stars
22. ▌
    PDF 2 · k-dense-ai bundle

    Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating new PDFs, filling PDF forms, encrypting/decrypting PDFs, extracting images, and OCR on scanned PDFs to make them searchable. If the user mentions a .pdf file or asks to produce one, use this skill.
    30.2k repo stars
23. ▌
    XLSX 2 · k-dense-ai bundle

    Create, edit, analyze, or convert Excel spreadsheets (.xlsx, .xlsm, .xltx) where the workbook file is the primary deliverable. Use for formulas, formatting, financial models, multi-sheet workbooks, and tabular cleanup exported to Excel. Also applies to .csv/.tsv when the user wants spreadsheet output. Do NOT use for Word documents, HTML reports, standalone Python scripts, database pipelines, or Google Sheets API work.
    30.2k repo stars
24. ▌
    Literature Review 2 · k-dense-ai bundle

    Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
    30.2k repo stars
25. ▌
    Scientific Slides 2 · k-dense-ai bundle

    Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
    30.2k repo stars
26. ▌
    Scientific Schematics 2 · k-dense-ai bundle

    Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.6 Flash for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
    30.2k repo stars
27. ▌
    Andrew Ng 2 · k-dense-ai bundle

    Applies the reasoning, principles, and frameworks of Andrew Ng (machine learning pioneer, co-founder of Coursera and DeepLearning.AI, Stanford University, and former Google Brain lead). Use this skill whenever the user is navigating AI application development, agentic workflows, automation strategy, AI-native software engineering, or rapid prototyping. Trigger this skill when discussing career advice in the AI era, evaluating AI regulations, structuring machine learning projects, or deciding how to integrate AI into a business. It emphasizes task-based automation, data-centric ML, and driving the cost of proof-of-concepts to zero.
    30.2k repo stars
28. ▌
    Jeff Dean 2 · k-dense-ai bundle

    Applies the engineering and research philosophies of Jeff Dean, Chief Scientist at Google DeepMind and Google Research. Reach for this skill whenever you are designing large-scale distributed systems, optimizing latency and energy efficiency, or making architectural decisions about machine learning infrastructure. It should trigger automatically for topics involving hardware-ML co-design, model distillation, sparse activation, massively multi-task models, or scaling systems by 5x to 10x. Use this skill to evaluate system bottlenecks, transition from specialized to unified models, and optimize experimental velocity. Apply his mental models to avoid premature 100x scaling and to treat AI models as reasoning engines rather than memorization databases.
    30.2k repo stars
29. ▌
    Fei Fei Li 2 · k-dense-ai bundle

    Applies the reasoning, frameworks, and mental models of Fei-Fei Li, computer vision pioneer, ImageNet creator, and co-director of Stanford HAI. Use this skill whenever Claude encounters topics related to AI ethics, human-centered AI, spatial intelligence, embodied AI, robotics, AI governance, diversity in tech, or the societal impacts of AI. Trigger this skill when users face decisions about AI product design (augment vs. replace), dataset formulation, navigating AI regulation, or choosing audacious research directions. Channel her pragmatic optimism and focus on spatial, physical grounding over pure language models.
    30.2k repo stars
30. ▌
    Kaiming He 2 · k-dense-ai bundle

    Applies the reasoning style of Kaiming He, computer vision pioneer and creator of ResNet. Use this skill whenever you are designing deep learning architectures, debugging neural network optimization, formulating generative AI problems, or bridging AI with other scientific domains. Trigger this skill for discussions on network depth, weight initialization, residual learning, flow matching, or when reframing discriminative tasks as conditional generation. It emphasizes simplicity in complex visual problems, end-to-end optimization, and viewing AI as a universal language for science.
    30.2k repo stars
31. ▌
    Yann Lecun 2 · k-dense-ai bundle

    This skill channels the reasoning of Yann LeCun, Chief AI Scientist at Meta and Turing Award winner. Use this skill whenever you are evaluating AI architectures, discussing the limitations of Large Language Models (LLMs), debating AI safety and regulation (anti-doomerism), or designing autonomous machine intelligence. It is highly relevant for topics involving self-supervised learning, open-source AI strategy, world models, physical grounding versus text-based learning, and objective-driven AI systems. Trigger this skill to apply his frameworks on abstract representation learning (JEPA) and energy-based models, even if the user doesn't explicitly name him.
    30.2k repo stars
32. ▌
    Judea Pearl 2 · k-dense-ai bundle

    Applies Judea Pearl's causal reasoning frameworks to distinguish correlation from causation, evaluate AI capabilities, and make counterfactual decisions. Reach for this skill whenever Claude encounters questions about causal inference, structural causal models, the limitations of deep learning, AGI, experimental design, covariate selection, or personalized decision-making. Trigger this skill for topics involving Bayesian networks, the do-calculus, the Ladder of Causation, or when a user tries to answer 'what if' or 'why' questions using purely observational data. Pearl's principles are essential for moving beyond probability calculus into true causal understanding.
    30.2k repo stars
33. ▌
    David Silver 2 · k-dense-ai bundle

    Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.
    30.2k repo stars
34. ▌
    Daphne Koller 2 · k-dense-ai bundle

    Applies the reasoning style of Daphne Koller (machine learning pioneer, co-founder of Coursera, founder and CEO of Insitro). Use this skill whenever you encounter problems involving AI and machine learning in biology, drug discovery, interdisciplinary collaboration, data generation vs. data mining, or transitioning from academia to industry. Trigger this skill when advising on career trade-offs, building cross-functional teams (especially bridging engineers and domain experts), designing data pipelines, evaluating causality vs. correlation, or applying AI to physical systems ('where bits meet atoms'). Channel her focus on fit-for-purpose data, pragmatism, and disproportionate leverage.
    30.2k repo stars
35. ▌
    Pieter Abbeel 2 · k-dense-ai bundle

    Applies the reasoning of Pieter Abbeel, robotics and reinforcement learning expert, UC Berkeley professor, and co-founder of Covariant. Use this skill whenever you are designing AI systems, tackling Sim2Real transfer, deploying machine learning in the physical world, or evaluating reinforcement learning architectures. Trigger this skill for questions about domain randomization, reward design, bootstrapping real-world AI, robotics hardware assumptions, or shifting from hard-coded rules to data-driven deep learning. It helps ground theoretical AI in physical embodiment and pragmatic deployment.
    30.2k repo stars
36. ▌
    Yoshua Bengio 2 · k-dense-ai bundle

    Applies the reasoning, AI safety frameworks, and deep learning principles of Yoshua Bengio (Turing Award winner, Mila). Reach for this skill whenever you are discussing AI safety, existential risk, deep learning architecture, representation learning, or AI governance. Trigger this skill when the user asks about mitigating AI risks, designing safe-by-design systems, evaluating frontier models, international AI coordination, or the fundamental mechanisms of intelligence (like compositionality and distributed representations). Use it to shift the focus from agentic reward-maximization to non-agentic 'Scientist AI', apply the precautionary principle to catastrophic risks, and emphasize mathematically rigorous guardrails.
    30.2k repo stars
37. ▌
    Demis Hassabis 2 · k-dense-ai bundle

    This skill channels the strategic and scientific reasoning of Demis Hassabis, CEO and co-founder of Google DeepMind, AlphaGo and AlphaFold, and 2024 Nobel Prize in Chemistry. Use this skill whenever you are evaluating AI for scientific discovery, tackling "root node" problems, designing reinforcement learning systems, or discussing AGI timelines, safety, and global governance. Reach for it when the user faces massive combinatorial search spaces, wants to apply AI to physical/biological sciences (like digital biology), or needs to balance rapid AI scaling with the rigorous scientific method. Apply these mental models to shift the focus from building consumer apps to using AI as the ultimate meta-solution for understanding reality.
    30.2k repo stars
38. ▌
    Ian Goodfellow 2 · k-dense-ai bundle

    Use this skill when reasoning about generative AI, adversarial machine learning, neural network security, algorithmic fairness, or deep learning fundamentals. This skill channels the thinking of Ian Goodfellow, inventor of Generative Adversarial Networks (GANs). Trigger this skill when the user asks about model robustness, mitigating bias, evaluating AI guardrails, designing generative models, or defending against adversarial attacks. Apply his frameworks of minimax games, adversarial feature learning, and worst-case robustness analysis to shift the user's perspective from average-case optimization to adversarial resilience.
    30.2k repo stars
39. ▌
    Ilya Sutskever 2 · k-dense-ai bundle

    Applies the reasoning style of Ilya Sutskever (deep learning pioneer, co-founder of OpenAI and Safe Superintelligence Inc.) to problems involving AI architecture, scaling laws, alignment, and research strategy. Reach for this skill whenever discussing machine learning paradigms, the limits of compute and data, AGI timelines, superintelligence safety, or deciding between hardcoding vs. learning. Trigger this skill for questions about next-word prediction, reinforcement learning efficiency, generalization gaps, and transitioning from brute-force scaling to fundamental research, even if the user doesn't explicitly name him.
    30.2k repo stars
40. ▌
    Stuart Russell 2 · k-dense-ai bundle

    Applies the reasoning of Stuart Russell, AI safety expert, UC Berkeley professor, and co-author of 'Artificial Intelligence: A Modern Approach'. Reach for this skill whenever evaluating AI safety, value alignment, the control problem, existential risk, AI regulation, or autonomous weapons. Use this when the user is discussing objective uncertainty, reinforcement learning risks, AI governance, or the societal impacts of AGI. Trigger this skill to apply his frameworks on provably beneficial AI, assistance games, and red-line regulation, ensuring AI systems remain deferential, uncertain of their objectives, and strictly aligned with human preferences.
    30.2k repo stars
41. ▌
    Andrej Karpathy 2 · k-dense-ai bundle

    Applies the mental models and frameworks of Andrej Karpathy (deep learning, former Director of AI at Tesla, founding member of OpenAI, Eureka Labs). Use this skill whenever you are helping the user build neural networks from scratch, debug deep learning pipelines, evaluate AI agent workflows, design LLM apps, or navigate the transition to Software 3.0 (vibe coding). It is highly relevant for pedagogy (untangling complex knowledge), assessing AI capabilities vs. limitations (jagged intelligence, tokenization limits), and architectural decisions (end-to-end optimization vs. complex pipelines). Reach for this whenever discussing LLM training, autonomous systems, or AI-assisted coding.
    30.2k repo stars
42. ▌
    Geoffrey Hinton 2 · k-dense-ai bundle

    Applies the reasoning style of Geoffrey Hinton, deep learning pioneer and 2018 Turing Award winner. Use this skill whenever evaluating AI safety, existential risk, neural network architectures, cognitive science, or tech regulation. Reach for this when the user is discussing LLM capabilities (understanding vs. autocomplete), the biological vs. digital intelligence divide, AI alignment strategies, or the societal/economic impacts of automation. It is highly applicable when dealing with contrarian scientific ideas, hardware/software integration (mortal vs. immortal computing), or global cooperation on technological threats. Do not wait for the user to name Hinton; trigger this skill proactively for any deep learning or AI existential risk analysis.
    30.2k repo stars
43. ▌
    Sebastian Thrun 2 · k-dense-ai bundle

    Applies the reasoning, principles, and mental models of Sebastian Thrun (robotics and self-driving cars pioneer, founder of Google X, Waymo, Udacity, Stanford University). Reach for this skill whenever Claude is asked to advise on hardware/software systems engineering, autonomous vehicles, moonshot ideation, probabilistic robotics (SLAM), or leading high-stakes engineering teams. Trigger this skill for discussions on democratizing education, regulating AI, transitioning from academic research to product development, or managing technical teams with empathy. Use it to shift focus from incremental component debates to end-to-end execution and audacious goals.
    30.2k repo stars
44. ▌
    Richard S Sutton 2 · k-dense-ai bundle

    Reach for this skill whenever you are discussing reinforcement learning, agentic AI systems, AI alignment, continual learning, or the philosophical limits of large language models. This skill channels the thinking of Richard S. Sutton (reinforcement learning pioneer, University of Alberta, Keen Technologies, 2024 Turing Award). Use it to evaluate AI architectures, make long-term AI prognostications, or design systems that learn from runtime experience rather than static datasets. Apply his frameworks when users ask about AGI, the 'Bitter Lesson' of computation, the Reward Hypothesis, or decentralized cooperation versus centralized AI control.
    30.2k repo stars
45. ▌
    Jurgen Schmidhuber 2 · k-dense-ai bundle

    Applies the reasoning, principles, and frameworks of Jürgen Schmidhuber (LSTM co-inventor and deep learning pioneer). Reach for this skill whenever tackling problems involving sequence learning, artificial curiosity, intrinsic motivation, reinforcement learning architectures, or predicting long-term technological and cosmic evolution. Use this when discussing AGI timelines, the history and attribution of AI breakthroughs, data compression as learning, or when designing autonomous agents that must set their own goals. Trigger this skill for topics like recurrent neural networks, algorithmic information theory, open-source AI democratization, and evaluating true existential risks versus media hype.
    30.2k repo stars
46. ▌
    Christopher Manning 2 · k-dense-ai bundle

    Applies the reasoning, architectural principles, and AI philosophy of Christopher Manning (natural language processing expert, Stanford University, director of Stanford AI Lab). Use this skill whenever you are discussing natural language processing, LLM architecture, AI research strategy, cognitive science, or the evolution of machine learning. Trigger this skill for questions about AGI timelines, academic vs. industry research trade-offs, linguistic structure in neural networks, modularity in AI design, or evaluating true intelligence versus mere memorization. Channel his pragmatic focus on domain science, adaptability, and competing on ideas rather than raw compute.
    30.2k repo stars
47. ▌
    Plain Language Summary · k-dense-ai

    Rewrite dense or technical text into a clear plain-language summary with a fixed structure (TL;DR, why it matters, key points, caveats). Use when the user asks to summarize, simplify, explain, "put this in plain language", or make something readable for a general / non-expert audience.
    30.2k repo stars
48. ▌
    Executing Analysis · k-dense-ai

    Use when you have a pre-registered analysis plan to execute inline in this session with review checkpoints, on a platform without subagents
    30.2k repo stars
49. ▌
    Surveying Prior Work · k-dense-ai

    Use after framing a question and before designing an analysis, or when choosing a method, judging whether a result is novel, or needing a prior effect size for a power calculation
    30.2k repo stars
50. ▌
    Designing The Analysis · k-dense-ai

    Use when you have an approved research question and need a concrete analysis plan, before touching outcome data or fitting any model
    30.2k repo stars
51. ▌
    Writing Science Skills · k-dense-ai

    Use when creating new skills, editing existing skills, or verifying skills work before deployment
    30.2k repo stars
52. ▌
    Preregistering Analysis · k-dense-ai bundle

    Use before running any confirmatory analysis or looking at outcome data, when testing a hypothesis, computing a p-value, or about to claim an effect - locks predictions and decision rules before results are seen
    30.2k repo stars
53. ▌
    Subagent Driven Analysis · k-dense-ai bundle

    Use when executing a pre-registered analysis plan with mostly independent steps in the current session
    30.2k repo stars
54. ▌
    Receiving Critical Review · k-dense-ai

    Use when receiving critical feedback on an analysis or manuscript, before implementing suggestions, especially if feedback seems unclear or methodologically questionable - requires verification, not performative agreement or blind changes
    30.2k repo stars
55. ▌
    Using Science Superpowers · k-dense-ai bundle

    Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions
    30.2k repo stars
56. ▌
    Framing Research Questions · k-dense-ai

    You MUST use this before any data analysis or investigation - before exploring a dataset, loading or profiling data, running a model, computing a statistic, or testing an idea, and before any outcome data is touched
    30.2k repo stars
57. ▌
    Requesting Red Team Review · k-dense-ai bundle

    Use after completing an analysis or before reporting a finding, to have a skeptical reviewer attack the conclusion before you believe it
    30.2k repo stars
58. ▌
    Establishing Feasibility First · k-dense-ai

    Use when your human partner has explicitly opted into exploratory or feasibility mode - a compute-heavy simulation, an unproven pipeline, an unbenchmarked solver, an untested cluster job - or when whether the work can run at all is still unknown, when a plan's largest configuration has never been executed, when a memory or wall-clock ceiling is estimated rather than measured, or when someone proposes pre-registering over runs that have never happened
    30.2k repo stars
59. ▌
    Investigating Anomalous Results · k-dense-ai

    Use when a result is surprising, impossible, contradicts a sanity check, a pipeline fails, a model won't converge, or a replication fails - before adjusting anything
    30.2k repo stars
60. ▌
    Reporting And Archiving Findings · k-dense-ai

    Use when an analysis is complete and verified, and you need to decide how to report it and archive the work for reproducibility
    30.2k repo stars
61. ▌
    Setting Up Reproducible Analysis · k-dense-ai

    Use when starting analysis work that needs isolation, or before executing a pre-registered plan - ensures an isolated, reproducible workspace with pinned environment, fixed seeds, and immutable raw data
    30.2k repo stars
62. ▌
    Verifying Results Before Claiming · k-dense-ai

    Use when about to claim a result, effect, significance, or that an analysis reproduces, before reporting or writing it up - requires running the analysis fresh and reading the actual output first; evidence before claims always
    30.2k repo stars
63. ▌
    Dispatching Parallel Investigations · k-dense-ai

    Use when facing 2+ independent investigations that can proceed without shared state - parallel literature survey, multi-dataset replication, or pre-specified robustness checks
    30.2k repo stars
64. ▌
    Andrew Ng · k-dense-ai bundle

    Applies the reasoning, principles, and frameworks of Andrew Ng (machine learning pioneer, co-founder of Coursera and DeepLearning.AI, Stanford University, and former Google Brain lead). Use this skill whenever the user is navigating AI application development, agentic workflows, automation strategy, AI-native software engineering, or rapid prototyping. Trigger this skill when discussing career advice in the AI era, evaluating AI regulations, structuring machine learning projects, or deciding how to integrate AI into a business. It emphasizes task-based automation, data-centric ML, and driving the cost of proof-of-concepts to zero.
    30.2k repo stars
65. ▌
    Jeff Dean · k-dense-ai bundle

    Applies the engineering and research philosophies of Jeff Dean, Chief Scientist at Google DeepMind and Google Research. Reach for this skill whenever you are designing large-scale distributed systems, optimizing latency and energy efficiency, or making architectural decisions about machine learning infrastructure. It should trigger automatically for topics involving hardware-ML co-design, model distillation, sparse activation, massively multi-task models, or scaling systems by 5x to 10x. Use this skill to evaluate system bottlenecks, transition from specialized to unified models, and optimize experimental velocity. Apply his mental models to avoid premature 100x scaling and to treat AI models as reasoning engines rather than memorization databases.
    30.2k repo stars
66. ▌
    Fei Fei Li · k-dense-ai bundle

    Applies the reasoning, frameworks, and mental models of Fei-Fei Li, computer vision pioneer, ImageNet creator, and co-director of Stanford HAI. Use this skill whenever Claude encounters topics related to AI ethics, human-centered AI, spatial intelligence, embodied AI, robotics, AI governance, diversity in tech, or the societal impacts of AI. Trigger this skill when users face decisions about AI product design (augment vs. replace), dataset formulation, navigating AI regulation, or choosing audacious research directions. Channel her pragmatic optimism and focus on spatial, physical grounding over pure language models.
    30.2k repo stars
67. ▌
    Kaiming He · k-dense-ai bundle

    Applies the reasoning style of Kaiming He, computer vision pioneer and creator of ResNet. Use this skill whenever you are designing deep learning architectures, debugging neural network optimization, formulating generative AI problems, or bridging AI with other scientific domains. Trigger this skill for discussions on network depth, weight initialization, residual learning, flow matching, or when reframing discriminative tasks as conditional generation. It emphasizes simplicity in complex visual problems, end-to-end optimization, and viewing AI as a universal language for science.
    30.2k repo stars
68. ▌
    Yann Lecun · k-dense-ai bundle

    This skill channels the reasoning of Yann LeCun, Chief AI Scientist at Meta and Turing Award winner. Use this skill whenever you are evaluating AI architectures, discussing the limitations of Large Language Models (LLMs), debating AI safety and regulation (anti-doomerism), or designing autonomous machine intelligence. It is highly relevant for topics involving self-supervised learning, open-source AI strategy, world models, physical grounding versus text-based learning, and objective-driven AI systems. Trigger this skill to apply his frameworks on abstract representation learning (JEPA) and energy-based models, even if the user doesn't explicitly name him.
    30.2k repo stars
69. ▌
    Judea Pearl · k-dense-ai bundle

    Applies Judea Pearl's causal reasoning frameworks to distinguish correlation from causation, evaluate AI capabilities, and make counterfactual decisions. Reach for this skill whenever Claude encounters questions about causal inference, structural causal models, the limitations of deep learning, AGI, experimental design, covariate selection, or personalized decision-making. Trigger this skill for topics involving Bayesian networks, the do-calculus, the Ladder of Causation, or when a user tries to answer 'what if' or 'why' questions using purely observational data. Pearl's principles are essential for moving beyond probability calculus into true causal understanding.
    30.2k repo stars
70. ▌
    David Silver · k-dense-ai bundle

    Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.
    30.2k repo stars
71. ▌
    Daphne Koller · k-dense-ai bundle

    Applies the reasoning style of Daphne Koller (machine learning pioneer, co-founder of Coursera, founder and CEO of Insitro). Use this skill whenever you encounter problems involving AI and machine learning in biology, drug discovery, interdisciplinary collaboration, data generation vs. data mining, or transitioning from academia to industry. Trigger this skill when advising on career trade-offs, building cross-functional teams (especially bridging engineers and domain experts), designing data pipelines, evaluating causality vs. correlation, or applying AI to physical systems ('where bits meet atoms'). Channel her focus on fit-for-purpose data, pragmatism, and disproportionate leverage.
    30.2k repo stars
72. ▌
    Pieter Abbeel · k-dense-ai bundle

    Applies the reasoning of Pieter Abbeel, robotics and reinforcement learning expert, UC Berkeley professor, and co-founder of Covariant. Use this skill whenever you are designing AI systems, tackling Sim2Real transfer, deploying machine learning in the physical world, or evaluating reinforcement learning architectures. Trigger this skill for questions about domain randomization, reward design, bootstrapping real-world AI, robotics hardware assumptions, or shifting from hard-coded rules to data-driven deep learning. It helps ground theoretical AI in physical embodiment and pragmatic deployment.
    30.2k repo stars
73. ▌
    Yoshua Bengio · k-dense-ai bundle

    Applies the reasoning, AI safety frameworks, and deep learning principles of Yoshua Bengio (Turing Award winner, Mila). Reach for this skill whenever you are discussing AI safety, existential risk, deep learning architecture, representation learning, or AI governance. Trigger this skill when the user asks about mitigating AI risks, designing safe-by-design systems, evaluating frontier models, international AI coordination, or the fundamental mechanisms of intelligence (like compositionality and distributed representations). Use it to shift the focus from agentic reward-maximization to non-agentic 'Scientist AI', apply the precautionary principle to catastrophic risks, and emphasize mathematically rigorous guardrails.
    30.2k repo stars
74. ▌
    Demis Hassabis · k-dense-ai bundle

    This skill channels the strategic and scientific reasoning of Demis Hassabis, CEO and co-founder of Google DeepMind, AlphaGo and AlphaFold, and 2024 Nobel Prize in Chemistry. Use this skill whenever you are evaluating AI for scientific discovery, tackling "root node" problems, designing reinforcement learning systems, or discussing AGI timelines, safety, and global governance. Reach for it when the user faces massive combinatorial search spaces, wants to apply AI to physical/biological sciences (like digital biology), or needs to balance rapid AI scaling with the rigorous scientific method. Apply these mental models to shift the focus from building consumer apps to using AI as the ultimate meta-solution for understanding reality.
    30.2k repo stars
75. ▌
    Ian Goodfellow · k-dense-ai bundle

    Use this skill when reasoning about generative AI, adversarial machine learning, neural network security, algorithmic fairness, or deep learning fundamentals. This skill channels the thinking of Ian Goodfellow, inventor of Generative Adversarial Networks (GANs). Trigger this skill when the user asks about model robustness, mitigating bias, evaluating AI guardrails, designing generative models, or defending against adversarial attacks. Apply his frameworks of minimax games, adversarial feature learning, and worst-case robustness analysis to shift the user's perspective from average-case optimization to adversarial resilience.
    30.2k repo stars
76. ▌
    Ilya Sutskever · k-dense-ai bundle

    Applies the reasoning style of Ilya Sutskever (deep learning pioneer, co-founder of OpenAI and Safe Superintelligence Inc.) to problems involving AI architecture, scaling laws, alignment, and research strategy. Reach for this skill whenever discussing machine learning paradigms, the limits of compute and data, AGI timelines, superintelligence safety, or deciding between hardcoding vs. learning. Trigger this skill for questions about next-word prediction, reinforcement learning efficiency, generalization gaps, and transitioning from brute-force scaling to fundamental research, even if the user doesn't explicitly name him.
    30.2k repo stars
77. ▌
    Linda Griffith · k-dense-ai bundle

    Apply the bioengineering, translational systems biology, and tissue modeling frameworks of Linda Griffith, Professor of Biological Engineering at MIT and tissue engineering pioneer. Use this skill whenever facing decisions, designs, or evaluations in bioengineering, tissue modeling, microphysiological systems (organs-on-chips), synthetic matrix design, disease subtyping, or drug target validation. Reach for this skill when evaluating preclinical models (human vs. animal), reframing overlooked or neglected pathologies into rigorous engineering challenges, selecting biomaterials, designing cell signal processing assays, or diagnosing operational flaws in experimental platforms (e.g., PDMS compound absorption or Matrigel lot variability).
    30.2k repo stars
78. ▌
    Stuart Russell · k-dense-ai bundle

    Applies the reasoning of Stuart Russell, AI safety expert, UC Berkeley professor, and co-author of 'Artificial Intelligence: A Modern Approach'. Reach for this skill whenever evaluating AI safety, value alignment, the control problem, existential risk, AI regulation, or autonomous weapons. Use this when the user is discussing objective uncertainty, reinforcement learning risks, AI governance, or the societal impacts of AGI. Trigger this skill to apply his frameworks on provably beneficial AI, assistance games, and red-line regulation, ensuring AI systems remain deferential, uncertain of their objectives, and strictly aligned with human preferences.
    30.2k repo stars
79. ▌
    Andrej Karpathy · k-dense-ai bundle

    Applies the mental models and frameworks of Andrej Karpathy (deep learning, former Director of AI at Tesla, founding member of OpenAI, Eureka Labs). Use this skill whenever you are helping the user build neural networks from scratch, debug deep learning pipelines, evaluate AI agent workflows, design LLM apps, or navigate the transition to Software 3.0 (vibe coding). It is highly relevant for pedagogy (untangling complex knowledge), assessing AI capabilities vs. limitations (jagged intelligence, tokenization limits), and architectural decisions (end-to-end optimization vs. complex pipelines). Reach for this whenever discussing LLM training, autonomous systems, or AI-assisted coding.
    30.2k repo stars
80. ▌
    Geoffrey Hinton · k-dense-ai bundle

    Applies the reasoning style of Geoffrey Hinton, deep learning pioneer and 2018 Turing Award winner. Use this skill whenever evaluating AI safety, existential risk, neural network architectures, cognitive science, or tech regulation. Reach for this when the user is discussing LLM capabilities (understanding vs. autocomplete), the biological vs. digital intelligence divide, AI alignment strategies, or the societal/economic impacts of automation. It is highly applicable when dealing with contrarian scientific ideas, hardware/software integration (mortal vs. immortal computing), or global cooperation on technological threats. Do not wait for the user to name Hinton; trigger this skill proactively for any deep learning or AI existential risk analysis.
    30.2k repo stars
81. ▌
    J Brandon Dixon · k-dense-ai bundle

    Apply the bioengineering, mechanobiology, and lymphatic transport reasoning of J. Brandon Dixon, professor of mechanical and biomedical engineering at Georgia Institute of Technology. Reach for this skill whenever analyzing lymphatic biomechanics, active vessel contractility versus passive drainage, peristaltic fluid transport, microfluidic organ-on-a-chip design, preclinical lymphedema models, non-invasive functional imaging, targeted nanomedicine delivery, or automated disease staging. Use this skill to critique bioengineering assumptions, guide quantitative protocol design, evaluate biomechanical pump failure, and formulate interdisciplinary biomedical solutions.
    30.2k repo stars
82. ▌
    Sebastian Thrun · k-dense-ai bundle

    Applies the reasoning, principles, and mental models of Sebastian Thrun (robotics and self-driving cars pioneer, founder of Google X, Waymo, Udacity, Stanford University). Reach for this skill whenever Claude is asked to advise on hardware/software systems engineering, autonomous vehicles, moonshot ideation, probabilistic robotics (SLAM), or leading high-stakes engineering teams. Trigger this skill for discussions on democratizing education, regulating AI, transitioning from academic research to product development, or managing technical teams with empathy. Use it to shift focus from incremental component debates to end-to-end execution and audacious goals.
    30.2k repo stars
83. ▌
    Richard S Sutton · k-dense-ai bundle

    Reach for this skill whenever you are discussing reinforcement learning, agentic AI systems, AI alignment, continual learning, or the philosophical limits of large language models. This skill channels the thinking of Richard S. Sutton (reinforcement learning pioneer, University of Alberta, Keen Technologies, 2024 Turing Award). Use it to evaluate AI architectures, make long-term AI prognostications, or design systems that learn from runtime experience rather than static datasets. Apply his frameworks when users ask about AGI, the 'Bitter Lesson' of computation, the Reward Hypothesis, or decentralized cooperation versus centralized AI control.
    30.2k repo stars
84. ▌
    Jurgen Schmidhuber · k-dense-ai bundle

    Applies the reasoning, principles, and frameworks of Jürgen Schmidhuber (LSTM co-inventor and deep learning pioneer). Reach for this skill whenever tackling problems involving sequence learning, artificial curiosity, intrinsic motivation, reinforcement learning architectures, or predicting long-term technological and cosmic evolution. Use this when discussing AGI timelines, the history and attribution of AI breakthroughs, data compression as learning, or when designing autonomous agents that must set their own goals. Trigger this skill for topics like recurrent neural networks, algorithmic information theory, open-source AI democratization, and evaluating true existential risks versus media hype.
    30.2k repo stars
85. ▌
    Christopher Manning · k-dense-ai bundle

    Applies the reasoning, architectural principles, and AI philosophy of Christopher Manning (natural language processing expert, Stanford University, director of Stanford AI Lab). Use this skill whenever you are discussing natural language processing, LLM architecture, AI research strategy, cognitive science, or the evolution of machine learning. Trigger this skill for questions about AGI timelines, academic vs. industry research trade-offs, linguistic structure in neural networks, modularity in AI design, or evaluating true intelligence versus mere memorization. Channel his pragmatic focus on domain science, adaptability, and competing on ideas rather than raw compute.
    30.2k repo stars
86. ▌
    Boltz · k-dense-ai bundle

    Cofold protein-ligand, protein-protein, and nucleic-acid complexes with Boltz-2, and predict binding affinity with its trained affinity head. Use this skill to build Boltz input YAML, run structure prediction with MSAs, pocket constraints, templates, and modified residues, screen compound libraries by cofolding, and interpret confidence scores (pLDDT, pTM, ipTM, PDE) and affinity output (binder probability and log10 IC50). Also trigger on Boltz, Boltz-1, Boltz-2, cofolding, boltz predict, affinity_pred_value, affinity_probability_binary, ipTM, or open-weights AlphaFold3 alternatives.
    30.2k repo stars
87. ▌
    Chembl · k-dense-ai bundle

    Query the ChEMBL database web services for measured bioactivity data, compound records and calculated properties, targets, assays, mechanisms of action, drug indications and warnings. Use this skill to build curated SAR or QSAR datasets for a target, look compounds up by SMILES, InChIKey, name, or ChEMBL id, run similarity and substructure searches, and check what chemistry is already known against a protein. Also trigger when a query mentions ChEMBL ids (CHEMBL...), pChEMBL values, IC50/Ki/Kd/EC50 retrieval, assay confidence scores, or ebi.ac.uk/chembl.
    30.2k repo stars
88. ▌
    Openfda · k-dense-ai bundle

    Query the FDA's public openFDA APIs for post-market drug data — FAERS adverse-event reports, Drugs@FDA approval and submission history, Structured Product Labels including boxed warnings, the National Drug Code directory, recall enforcement reports, and drug shortages. Use this skill to check what a regulator has already concluded about a molecule or its class, to date an approval and count its efficacy supplements, to read an approved indication or boxed warning, and to score a drug-event pair for disproportionate reporting with PRR, ROR, and chi-squared. Also trigger on openFDA, api.fda.gov, FAERS, Drugs@FDA, SPL, NDC, pharmacovigilance, boxed warning, adverse event report, drug recall, or safety signal.
    30.2k repo stars
89. ▌
    Degraders · k-dense-ai bundle

    Work on bifunctional degraders and molecular glues, where potency comes from a ternary complex rather than occupancy. Use this skill to apply the property rules that govern this beyond-rule-of-five space, reason about linker length, attachment vector and E3 ligase choice, prepare inputs for ternary complex structure prediction, and interpret degradation readouts — DC50, Dmax, cooperativity, and the hook effect that makes a dose-response curve turn over. Also trigger on PROTAC, molecular glue, targeted protein degradation, E3 ligase, cereblon, VHL, ternary complex, DC50, Dmax, hook effect, cooperativity, or PROTAC-DB.
    30.2k repo stars
90. ▌
    Open Targets · k-dense-ai bundle

    Query the Open Targets Platform GraphQL API for target-disease associations, genetic and clinical evidence, tractability and safety liabilities, target prioritisation metrics, known drugs and mechanisms of action, and disease ontology. Use this skill for target identification and validation, target-disease evidence review, druggability assessment, drug repurposing, and resolving gene, disease, and drug names to Ensembl, MONDO, and ChEMBL identifiers. Also trigger when a query mentions Open Targets, platform.opentargets.org, association scores, tractability buckets, or api.platform.opentargets.org.
    30.2k repo stars
91. ▌
    Uniprot Rcsb · k-dense-ai bundle

    Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.
    30.2k repo stars
92. ▌
    Autodock Vina · k-dense-ai bundle

    Structure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prepare receptors and ligands as PDBQT, run single or batch docking, rescore, and interpret affinities, poses, and ligand efficiency. Covers box definition from a reference ligand or pocket residues, protonation and tautomer decisions, flexible side chains, exhaustiveness and seeds, redocking validation, and virtual screening over compound libraries. Also trigger on vina, smina, gnina, mk_prepare_ligand, mk_prepare_receptor, mk_export, scrub.py, PDBQT, autogrid4, docking box, or binding-pose prediction.
    30.2k repo stars
93. ▌
    Target Safety · k-dense-ai bundle

    Assemble the human genetic evidence for and against a target before a programme commits to it — the evidence class that most improves the odds of surviving clinical development. Use this skill to pull gnomAD constraint metrics (LOEUF, pLI, observed/expected) that show whether loss of function is tolerated in people, retrieve GWAS Catalog associations and fine-mapped credible sets for a gene, and read a natural human knockout as a safety readout. Also trigger on gnomAD, LOEUF, pLI, loss-of-function intolerance, mutational constraint, GWAS Catalog, credible set, human knockout, genetic support, or target safety dossier.
    30.2k repo stars
94. ▌
    Chemical Space · k-dense-ai bundle

    Navigate make-on-demand catalogues — ZINC-22 through CartBlanche and Enamine REAL Space — to find compounds that can actually be ordered. Use this skill to look substances up by ZINC identifier or structure, understand tranche partitioning by heavy-atom count and logP, and choose between screening an enumerated subset and searching a combinatorial synthon space with a fragment-growing method such as V-SYNTHES. Also trigger on ZINC22, CartBlanche, Enamine REAL, make-on-demand, tangible library, synthon, tranche, giga-scale enumeration, or ultra-large virtual screening.
    30.2k repo stars
95. ▌
    Clinicaltrials · k-dense-ai bundle

    Search the ClinicalTrials.gov registry through its version 2 REST API for interventional and observational studies, their phases, enrolment, endpoints, sponsors, and posted results. Use this skill to survey who is developing what against an indication, date a competitor's programme, read primary and secondary outcome measures, find eligibility criteria, and distinguish a study that completed from one that was terminated or withdrawn. Also trigger on ClinicalTrials.gov, NCT number, trial registry, study phase, enrolment, primary outcome measure, recruiting status, trial sponsor, or competitive landscape.
    30.2k repo stars
96. ▌
    Immunogenicity · k-dense-ai bundle

    Estimate how likely a protein therapeutic is to provoke an anti-drug antibody response, and locate the sequence regions responsible. Use this skill to tile a sequence into peptides, predict class II MHC presentation across a population-representative allele panel, aggregate predicted binders into a per-region and whole-molecule risk score, compare a candidate against its closest human germline, and decide which liabilities are worth deimmunising. Also trigger on immunogenicity, anti-drug antibody, ADA, T-cell epitope, MHC class II, HLA-DRB1, NetMHCIIpan, NetMHCpan, deimmunisation, tregitope, or population coverage.
    30.2k repo stars
97. ▌
    Retrosynthesis · k-dense-ai bundle

    Plan synthetic routes and judge whether a proposed molecule can actually be made, using AiZynthFinder's Monte-Carlo tree search over template-derived reactions and a purchasable building-block stock. Use this skill to configure expansion and filter policies, choose a stock file, run route search over a candidate set, and read the returned trees — solved fraction, route depth, and which building blocks a route bottoms out in. Also trigger on AiZynthFinder, retrosynthetic tree search, synthetic accessibility, SAscore, RAscore, building-block stock, reaction template, or route scoring.
    30.2k repo stars
98. ▌
    Admet Prediction · k-dense-ai bundle

    Turn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a developability verdict rather than a table of numbers. Use this skill to run batch prediction over a library, interpret each endpoint against its DrugBank-approved percentile, and flag the liabilities that stop a series — hERG blockade, CYP inhibition, poor Caco-2 permeability, high clearance, and plasma protein binding. Also trigger on ADMET-AI, admet_ai, Chemprop-RDKit, hERG liability, CYP3A4 inhibition, Caco-2, bioavailability prediction, or developability triage.
    30.2k repo stars
99. ▌
    Oligonucleotides · k-dense-ai bundle

    Design small interfering RNA and antisense oligonucleotide sequences against a transcript, and screen them for the failure modes specific to nucleic-acid drugs. Use this skill to tile a target transcript, apply positional and thermodynamic selection rules including duplex asymmetry and nearest-neighbour melting temperature, scan candidates for seed-region complementarity to off-target transcripts, and lay out a chemical modification pattern — gapmer architecture, 2'-O-methyl and 2'-MOE wings, locked nucleic acid, and phosphorothioate placement. Also trigger on siRNA, antisense oligonucleotide, ASO, gapmer, RNase H, seed region, duplex asymmetry, 2'-MOE, locked nucleic acid, phosphorothioate, or GalNAc conjugate.
    30.2k repo stars
100. ▌
     Patent Landscape · k-dense-ai bundle

     Find out whether a chemical series is already claimed, using SureChEMBL's patent-extracted compound corpus and, where a key is available, PatentsView for legal status and assignee history. Use this skill to trace a structure to the patent documents that disclose it, survey an assignee's filings around a target, and understand what the freedom-to-operate question requires that a structure search cannot answer. Also trigger on SureChEMBL, patent chemistry, Markush structure, freedom to operate, composition of matter, assignee, priority date, patent family, or PatentsView.
     30.2k repo stars