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Citation-grade academic literature retrieval (search, semantic chunks, byte-range read, figure fetch) over Sciverse, an open scientific platform indexing peer-reviewed and preprint papers.
Multi-Omics Integration - Integrate transcriptomics (TCGA), proteomics (UniProt), pathway enrichment (STRING), and metabolic pathway (KEGG) data for a target gene. Outputs a unified JSON report combining expression profiles, protein annotations, enriched…
ADMET & Drug-Likeness Report - Generate comprehensive ADMET and drug-likeness report: molecular properties, H-bond analysis, hydrophobicity, topology, and ADMET prediction. Use this skill for medicinal chemistry tasks involving calculate mol basic info…
Affinity Maturation Pipeline - Affinity maturation: compute binding affinity, predict mutations, compute hydrophilicity, and predict drug-target interaction. Use this skill for antibody engineering tasks involving ComputeAffinityCalculator zero shot sequence…
Alanine Scanning Mutagenesis Pipeline - Alanine scanning: design scan, compute properties for each mutant, predict interactions, and compare. Use this skill for protein biochemistry tasks involving AlanineScanningDesigner ComputeProtPara…
Ring System Analysis - Analyze ring systems: count aliphatic carbocycles, analyze aromaticity, compute topology, and structure complexity. Use this skill for organic chemistry tasks involving GetAliphaticCarbocyclesNum AromaticityAnalyzer calculate mol…
AlphaFold Structure Analysis Pipeline - AlphaFold pipeline: download predicted structure, predict pockets, extract sequence, and compute properties. Use this skill for computational biology tasks involving download alphafold structure run fpocket extract pdb…
Antibody Drug Development - Develop antibody drug: target protein analysis, biotherapeutic lookup, protein properties, and interaction prediction. Use this skill for biologics tasks involving get uniprotkb entry by accession get biotherapeutic by name…
Antibody-Target Analysis - Analyze an antibody target: UniProt protein info, InterPro domains, protein properties, and biotherapeutic data from ChEMBL. Use this skill for immunology tasks involving get uniprotkb entry by accession query interpro…
ATC Drug Classification Lookup - Look up drug in ATC classification: ChEMBL ATC class, FDA drug info, PubChem compound, and mechanism of action. Use this skill for pharmacology tasks involving get atc class by level5 get mechanism of action by drug name get…
Binding Site Characterization - Characterize binding sites: predict pockets with fpocket and P2Rank, get binding site info from ChEMBL, and visualize. Use this skill for structural biology tasks involving run fpocket pred pocket prank get binding site by id…
Bioassay Data Analysis - Analyze bioassay data: PubChem assay summary, ChEMBL activity search, compound properties, and target info. Use this skill for bioassay science tasks involving get assay summary by cid search activity calculate mol basic info get…
Biomarker Discovery Pipeline - Discover biomarkers: TCGA differential expression, NCBI gene data, OpenTargets associations, and clinical relevance. Use this skill for precision medicine tasks involving tcga differential expression analysis get gene metadata…
BioSample & Genome Cross-Reference - Cross-reference biosample and genome data: NCBI biosample, genome report, sequence reports, and taxonomy. Use this skill for genomics tasks involving get biosample report get genome dataset report by accession get genome…
BLAST & Protein Analysis Pipeline - BLAST search followed by comprehensive protein analysis: BLAST, then structure prediction, properties, and function. Use this skill for sequence bioinformatics tasks involving blast search pred protein structure esmfold…
Cancer Therapy Design - Design cancer therapy: identify targets, find drugs, check safety, and analyze differential expression. Use this skill for oncology tasks involving get associated targets by disease efoId get associated drugs by target name get adverse…
CAS Number Compound Lookup - Look up compounds by CAS: convert CAS to price/availability, get PubChem data, get ChEMBL info, and structure analysis. Use this skill for chemical information tasks involving CASToPrice get compound by name get molecule by name…
Cell Line Assay Analysis - Analyze cell line assays: ChEMBL cell line info, assay search, activity data, and target info. Use this skill for cell biology tasks involving get cell line by id search assay search activity get target by name. Combines 4 tools…
Chemical Patent & Novelty Analysis - Analyze chemical novelty: PubChem substructure CAS search, ChEMBL similarity search, compound synonyms, and literature. Use this skill for patent chemistry tasks involving get substructure cas get similarity by smiles get…
Chemical Property Profiling - Profile chemical properties: basic info, hydrophobicity, H-bonds, charges, and molecular complexity. Use this skill for physical chemistry tasks involving calculate mol basic info calculate mol hydrophobicity calculate mol hbond…
Chemical Safety Assessment - Assess chemical safety: PubChem compound info, FDA drug data, ADMET prediction, and structural alerts from ChEMBL. Use this skill for chemical safety tasks involving get general info by compound name get warnings and cautions by…
Chemical Structure Comparison - Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records. Use this skill for cheminformatics tasks involving NameToSMILES ChemicalStructureAnalyzer calculate smiles similarity…
Chromosome Structure Analysis - Analyze chromosome: NCBI summary, UCSC cytoband, genome sequence, and Ensembl assembly info. Use this skill for cytogenetics tasks involving get chromosome summary get cytoband get chromosome sequence get info assembly.…
Clinical Pharmacology Report - Generate clinical pharmacology report: PK, PD, mechanism, drug interactions, and special populations. Use this skill for clinical pharmacology tasks involving get pharmacokinetics by drug name get pharmacodynamics by drug name…
Clinical Trial Drug Profiling - Profile drug for clinical trials: FDA clinical studies, contraindications, pregnancy info, and geriatric use. Use this skill for clinical research tasks involving get clinical studies info by drug name get contraindications by…
Computational Analysis via Code Execution - Execute custom computational analysis code, analyze software, and search for reference implementations. Use this skill for computational science tasks involving exec code software analysis search dataset search…
Combinatorial Chemistry Library Design - Design combinatorial library: validate core SMILES, generate variants, compute properties, and predict ADMET for library. Use this skill for combinatorial chemistry tasks involving is valid smiles calculate mol basic…
Comparative Drug Analysis - Compare drugs: structure analysis, PubChem data, FDA safety, and ChEMBL bioactivity. Use this skill for comparative pharmacology tasks involving ChemicalStructureAnalyzer get compound by name get adverse reactions by drug name…
Cross-Database Compound Lookup - Cross-reference compound across databases: PubChem, ChEMBL, KEGG, and CAS number lookup. Use this skill for chemical information tasks involving get compound by name get molecule by name kegg find CASToPrice. Combines 4 tools…
Compound-to-Drug Analysis Pipeline - Full compound-to-drug pipeline: name-to-SMILES conversion, structure analysis, drug-likeness, and FDA drug lookup. Use this skill for drug development tasks involving NameToSMILES ChemicalStructureAnalyzer calculate mol…
Cross-Species Comparative Genomics - Compare genomes across species: Ensembl compara, alignment, gene trees, and NCBI taxonomy. Use this skill for comparative genomics tasks involving get info compara species sets get alignment region get genetree member…
Disease-Specific Compound Screening - Screen compounds for disease: get DLEPS score for disease relevance, predict ADMET, and check drug-likeness. Use this skill for drug discovery tasks involving calculate dleps score pred molecule admet calculate mol drug…
Disease-Drug Landscape Analysis - Map the drug landscape for a disease: OpenTargets disease drugs, FDA indications, and clinical studies. Use this skill for drug discovery tasks involving get associated drugs by target name get drug names by indication get…
Disease Knowledge Graph - Build disease knowledge graph: OpenTargets targets, drugs, publications, and phenotypes. Use this skill for disease informatics tasks involving get associated targets by disease efoId get associated drugs by target name get…
Disease Protein Profiling - Profile a disease protein: UniProt data, AlphaFold structure, InterPro domains, phenotype associations from Ensembl. Use this skill for medical proteomics tasks involving query uniprot download alphafold structure query interpro…
Drug-Indication Mapping - Map drug indications: ChEMBL drug indications, FDA indications, OpenTargets drug associations, and literature. Use this skill for clinical informatics tasks involving get drug indication by id get indications by drug name get…
Drug-Drug Interaction Checker - Check interactions between multiple drugs using FDA interaction data, PubChem compound info, and ChEMBL target overlap analysis. Use this skill for clinical pharmacology tasks involving get drug interactions by drug name get…
Drug Metabolism Study - Study drug metabolism: FDA metabolism data, ChEMBL metabolism records, PubChem compound data, and clinical pharmacology. Use this skill for drug metabolism tasks involving get metabolism by id get pharmacokinetics by drug name get…
Drug Repurposing Screening - Screen existing drugs for new indications by querying FDA indications, ChEMBL mechanisms, and OpenTargets drug-disease associations. Use this skill for drug discovery tasks involving get indications by drug name get mechanism of…
Comprehensive Drug Safety Profile - Build a complete drug safety profile by combining FDA adverse reactions, boxed warnings, drug interactions, and contraindications. Use this skill for pharmacology tasks involving get adverse reactions by drug name get boxed…
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