Science & Research
723 results
- Alterlab GlycoengineeringAlterLab Creative Technologies LaboratoryAnalyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing therapeutic-antibody or biologic glycoforms, or doing glycoprotein engineering and vaccine-design work.
- AlterLab-IEU/AlterLab-Academic-SkillsAlterLab Creative Technologies LaboratoryCollection242 evaluated academic Claude/agent skills across 18 research domains — bioinformatics, cheminformatics, data science, databases, clinical, social science, Turkish academia & more. Every skill ships an executable eval. Citation verifier, research→write→review pipeline, 7 multi-agent workflows. Claude Code plugins; also Cursor, Codex, Gemini CLI.
- Alterlab LigandmpnnAlterLab Creative Technologies LaboratoryDesign protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand.
- Alterlab MedchemAlterLab Creative Technologies LaboratoryApplies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PAINS or reactive groups, or assessing drug-likeness of candidate molecules. Part of the AlterLab Academic Skills suite.
- Alterlab Molecular DynamicsAlterLab Creative Technologies LaboratoryRuns and analyzes molecular dynamics simulations with OpenMM and MDAnalysis — setting up protein and small-molecule systems, assigning force fields, running energy minimization and production MD, and analyzing trajectories (RMSD, RMSF, contact maps, free energy surfaces).
- Alterlab PhylogeneticsAlterLab Creative Technologies LaboratoryBuild phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree.
- Alterlab ProteinmpnnAlterLab Creative Technologies LaboratoryDesign protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant.
- Alterlab PyopenmsAlterLab Creative Technologies LaboratoryBuild complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.
- Alterlab PytdcAlterLab Creative Technologies LaboratoryLoads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark dataset, applying scaffold or cold-split evaluation, or sourcing labeled molecules for ADMET, toxicity, or DTI modeling.
- Alterlab RdkitAlterLab Creative Technologies LaboratoryProvides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling.
- Alterlab RfdiffusionAlterLab Creative Technologies LaboratoryGenerate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functional motif into a fold, designing a binder backbone to a target surface, or building symmetric assemblies; RFdiffusion…
- Alterlab ScgptAlterLab Creative Technologies LaboratoryApply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData.
- Alterlab SympyAlterLab Creative Technologies LaboratorySymbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas.
- Alterlab TiledbvcfAlterLab Creative Technologies LaboratoryStore and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for flat VCF, building joint variant stores, or querying thousands of samples by region.
- Alterlab Torch GeometricAlterLab Creative Technologies LaboratoryGraph Neural Networks with PyTorch Geometric (PyG) — node and graph classification, link prediction, GCN, GAT, and GraphSAGE layers, heterogeneous graphs, and molecular property prediction. Use when building or training GNNs for geometric deep learning on graph-structured data. Part of the AlterLab Academic Skills suite.
- Alterlab TorchdrugAlterLab Creative Technologies LaboratoryBuilds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning.
- Julia ScientificplurigridJulia package equivalents for 137 K-Dense-AI scientific skills. Maps Python bioinformatics, chemistry, ML, quantum, and data science packages to native Julia ecosystem.
- Arxiv SearchyorkeccakSearch arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
- Biomedical SearchyorkeccakComplete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.
- Literature SearchyorkeccakComprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv. Natural language queries powered by Valyu semantic search.
- ykdojo/paper-searchYKCollectionClaude Code plugin for searching 250M+ academic papers via OpenAlex. Search by keyword, look up by DOI, sort by citations or date. No API key needed.
- Healthcare Providers EnrichNimbleFills gaps in existing healthcare practitioner lists — adds missing phone numbers, credentials, specialties, contact info, education, reviews, and regulatory data. Triggers: "enrich my provider list", "fill in missing data", "add phone numbers to these doctors", "complete this practitioner database", "enrich CRM export", "fill gaps in my provider data", "supplement this healthcare list".
- Scientific SchematicsovachieverCreate publication-quality scientific diagrams using Nano Banana Pro AI with iterative refinement. AI generation is the default method for all diagram types. Generates high-fidelity images with automatic quality review. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
- TooluniverseovachieverUse this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages.