Available Tools
Computational bioinformatics tools available in SmartsBio — AI protein design, sequence alignment, quality control, variant analysis, file processing, and more. Tools can be called directly via the API or invoked automatically by the agent.
Looking for database tools? Sequence search, protein databases, genomics, pathways, clinical data, literature, and patents are covered on the Available Databases page.
Sync
Results returned immediately via POST /v1/tools/:id/run. Best for fast, lightweight operations.
Pipeline
Async execution via POST /v1/pipelines. Get a pipeline ID immediately, then stream or poll. Used for compute-heavy tools.
Both
Supports either mode. A single long-running tool submitted to /v1/pipelines is valid — no multi-step chain required.
Tool Reference
71 tools across 46 categories. Tool IDs are stable across versions.
Structural Biology1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| molecular-docking | Molecular Docking | Blind molecular docking of small molecules onto protein targets using DiffDock-L (MIT, MIT/Stanford). Diffusion-based approach: automatically discovers binding pockets without prior knowledge. Success rate: 43% (RMSD <2Å), DockGen generalization benchmark: 22.6% — state-of-the-art blind docking. Generates multiple ranked docking pose candidates with confidence scores. Complements Chai-1 (co-folding from scratch); DiffDock-L docks onto an existing structure. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). Use for drug discovery: identify binding mode and rank ligand candidates. | Pipeline |
Proteomics11 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| molecular-dynamics | Molecular Dynamics Simulation | Run molecular dynamics (MD) simulation to validate protein stability using OpenMM (MIT/LGPL, Stanford). Simulates the protein in explicit water + ions at physiological conditions (300 K, 1 atm, 150 mM NaCl). Validates dynamic stability — ThermoMPNN checks static ΔΔG; OpenMM checks real behaviour over nanoseconds. OpenMM 8 supports ML potentials alongside physics-based force fields. Outputs: trajectory file, RMSD stability plot, per-residue flexibility (RMSF), and average structure PDB. Runtime: ~100–300 ns/day on g5.xlarge (A10G); 50–100 ns sufficient for stability validation. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). Cost: ~$3–10 per job. | Pipeline |
| protein-complex-prediction | Protein Complex Prediction | Predict the 3D structure of multi-molecule complexes using Chai-1 (Apache 2.0, ChaiDiscovery). Co-folds proteins, small molecules, nucleic acids, glycans, and ions simultaneously in one model. Protein-ligand: 77% success rate (vs AlphaFold3 76%). Protein-protein multimers: 75.1% DockQ (beats AlphaFold-Multimer 67.7%). Antibody-antigen: 47.9% DockQ in single-sequence mode. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). Use when you need multi-molecule complex structure prediction without an AlphaFold3 licence. | Pipeline |
| protein-sequence-codesign | Protein Sequence Co-design | Generate protein sequence and 3D structure simultaneously using DPLM-2 diffusion model. Performs true joint sequence+structure co-design in a single diffusion pass — no separate inverse folding step. Supports unconditional generation and motif-constrained scaffolding (design a protein around a fixed active site). 650M DPLM-2 model outperforms 3B-scale baselines (ICLR 2025 / ICML 2025 Spotlight). Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). Use for de novo protein generation or motif-anchored scaffold design. | Pipeline |
| protein-sequence-generation | Protein Sequence Generation | Generate diverse protein sequences within a protein family using ProGen2 (Salesforce, BSD-3). Trained on 1 billion protein sequences, ProGen2 produces natural-looking sequences that respect the evolutionary grammar of the target protein family. Provide a family name (e.g. "GFP", "serine protease") or a seed sequence, and the model generates diverse variants with perplexity scores for quality ranking. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). Ideal as a fast pre-screening step before expensive GPU design runs. | Pipeline |
| protein-sequence-infilling | Protein Sequence Infilling | Design protein scaffolds that preserve a required structural motif using DPLM-2 inverse folding. Given a PDB structure with a fixed functional site (e.g. catalytic triad, disulfide bonds, binding loop), generates diverse scaffold sequences that maintain the exact geometry of the fixed residues. Useful for enzyme engineering and epitope grafting where the active site geometry is non-negotiable. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). | Pipeline |
| protein-variant-scoring | Protein Variant Scoring | Zero-shot fitness scoring of protein variants using ProGen2 log-likelihood. Ranks point mutations (e.g. A123G), insertions, deletions, and combinatorial variants by their log-likelihood delta relative to the wildtype — no experimental training data required. Handles both substitutions AND indels, unlike most tools that only score substitutions. Ideal for pre-screening thousands of variants cheaply before committing to wet lab synthesis. Runs on GPU-accelerated AWS Batch (Spot g5.xlarge). BSD-3 license (Salesforce). | Pipeline |
| antibody-humanization | Antibody Humanization | Humanize antibody/nanobody sequences and score immunogenicity using BioPhi (MIT, Merck). Two complementary methods: Sapiens — deep learning CDR humanization while preserving binding specificity. OASis — 9-mer humanness scoring against Observed Antibody Space; correlates with clinical immunogenicity. Critical downstream step for all Boltz nanobody designs before therapeutic development. A nanobody with excellent binding but poor OASis humanness score will fail in clinical trials. Runs on ECS Fargate (CPU). Fast: 1–2 minutes per antibody. | Pipeline |
| protein-function-annotation | Protein Function Annotation | Predict protein function (GO terms) and enzyme class (EC number) using DeepFRI (BSD-3, Flatiron Institute). GCN on contact maps + protein language model features for accurate zero-shot function prediction. Predicts: Molecular Function (MF), Biological Process (BP), Cellular Component (CC), and EC class. Identifies functional residues — which specific amino acids drive each predicted GO term. Critical quality control: ensures designed proteins have the intended functional annotation. Runs on ECS Fargate (CPU). Fast: 1–3 minutes per protein. | Pipeline |
| protein-stability-prediction | Protein Stability Prediction | Predict thermodynamic stability change (ΔΔG) for protein point mutations using ThermoMPNN (UNC). ThermoMPNN-D extends prediction to double mutants. Fast CPU inference: screens hundreds of variants in under a minute. ΔΔG < 0 kcal/mol = stabilising mutation; ΔΔG > 0 = destabilising. Critical gatekeeper: filter unstable designs before committing to expensive GPU runs or wet lab synthesis. License: CC BY-ND 4.0 (allows commercial use and self-hosting; prohibits modifying the model itself). Runs on ECS Fargate (CPU). Fast: <1 minute for single scan. | Pipeline |
| string-db | STRING Database Tools | Comprehensive plugin for protein-protein interaction analysis using STRING database | Sync |
| uniprot-toolkit | UniProt Database Tools | Comprehensive plugin for UniProt protein database operations including search, fetch, and ID mapping | Sync |
Bowtie21 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| bowtie2-toolkit | Bowtie2 - Fast Read Alignment | Ultrafast and memory-efficient tool for aligning sequencing reads to large reference genomes. Supports both end-to-end and local alignment modes with comprehensive parameter control for various sequencing platforms and read types. | Pipeline |
Bwa1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| bwa-toolkit | BWA - Burrows-Wheeler Aligner | Fast and memory-efficient alignment tool for short DNA sequencing reads against large reference genomes using Burrows-Wheeler Transform. Supports multiple alignment algorithms and paired-end sequencing data with comprehensive parameter control. | Pipeline |
Hisat21 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| hisat2-toolkit | HISAT2 - Hierarchical Indexing for Spliced Alignment of Transcripts 2 | Fast and sensitive splice-aware alignment of RNA-seq reads to a reference genome using hierarchical graph-based indexing. | Pipeline |
3d Protein Structures1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| alphafold-db | AlphaFold 3D Protein Structure Database [PRIMARY FOR 3D STRUCTURES] | 🧬 PRIMARY TOOL FOR 3D PROTEIN STRUCTURE VISUALIZATION 🧬 AI-predicted 3D protein structure visualization and analysis. Access 214+ million protein structure predictions with confidence scores. ALWAYS USE THIS for 3D protein structures, molecular visualization, and structural analysis queries. | Sync |
Preprints3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| arxiv-search | arXiv Search | Search arXiv preprint repository for cutting-edge research and early-stage scientific papers | Sync |
| biorxiv-search | bioRxiv Search | Search bioRxiv preprint repository for cutting-edge biological research and early-stage life science papers | Sync |
| medrxiv-search | medRxiv Search | Search medRxiv preprint repository for cutting-edge health sciences research and early-stage medical papers | Sync |
Genomics4 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| biograph | Biograph Knowledge Graph | Query the Biograph Knowledge Graph for genes, proteins, diseases, variants, pathways, and drugs with their relationships | Sync |
| ensembl | Ensembl | Comprehensive plugin for Ensembl genome browser and annotation database - providing access to vertebrate genomic data | Sync |
| go-toolkit | Gene Ontology (GO) Toolkit | Comprehensive toolkit for Gene Ontology analysis including term search, annotations, and enrichment | Sync |
| ncbi-gene | NCBI-Gene | Search NCBI Gene database for gene information, locations, and annotations | Sync |
Chembl1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| chembl-toolkit | ChEMBL Database Tools | Comprehensive plugin for ChEMBL bioactivity database operations including compound search, target analysis, and drug discovery data | Sync |
Clinical Medicine3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| clinical-tables-toolkit | Clinical Tables Search Service | Comprehensive search across 25+ clinical and genomics tables from National Library of Medicine (NLM) including conditions, drugs, genes, variants, ICD codes, and medical terminology | Sync |
| clinical-trials-toolkit | Clinical Trials Database Tools | Comprehensive clinical trials search using ClinicalTrials.gov API v2 with 400,000+ registered trials worldwide | Sync |
| medical-devices-toolkit | Medical Devices & Procedures Tools | Medical device information from FDA (510k, PMA, recalls) and medical procedures/devices from SNOMED CT terminology | Sync |
Citations1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| crossref-search | CrossRef Search | DOI resolution, citation tracking, and comprehensive bibliographic data retrieval using CrossRef API | Sync |
Statistics1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| data-statistics | Data Statistics - Statistical Analysis of Data Files | Run comprehensive statistical analysis on workspace data files. Computes descriptive statistics (mean, SD, median, CI), performs group comparisons (t-test, ANOVA, pairwise Tukey), correlation analysis, and data quality metrics (outliers, missing values). Supports multiple testing correction (Bonferroni, Benjamini-Hochberg). Use when the user needs statistical tests, group comparisons, or a numerical summary of their data. | Sync |
Ebi1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ebi-job-dispatcher | EMBL-EBI Job Dispatcher Tools | Comprehensive plugin for EMBL-EBI Job Dispatcher framework providing access to 50+ bioinformatics analysis tools including BLAST, Clustal, InterProScan, and more | Pipeline |
Cross Database Search1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ebi-search | EBI Search Cross-Database Discovery Tools | Comprehensive plugin for EMBL-EBI Search providing unified cross-database search across 170+ biological datasets with faceted filtering and cross-reference exploration | Sync |
Bedtools1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| bedtools-toolkit | BEDTools - Genome Interval Analysis | Powerful suite for genome interval manipulation and analysis. BEDTools provides comprehensive functionality for intersecting, merging, counting, complementing and many other operations on genomic intervals in BED, GFF/GTF, VCF and BAM file formats. Essential for comparative genomics and functional annotation analysis. | Pipeline |
Format Conversion1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| format-conversion-toolkit | Format Conversion Toolkit | Comprehensive bioinformatics file format conversion toolkit. Converts between sequence formats (FASTA, FASTQ, GenBank, EMBL, AB1), alignment formats (SAM, BAM, CRAM, BED), variant formats (VCF, BCF), and annotation formats (GFF3, GTF, BED). Supports single files, multiple files, and automatic extraction of zip/tar archives. | Pipeline |
Genomicranges1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| genomicranges-toolkit | GenomicRanges - Bioconductor Genomic Intervals | Comprehensive genomic interval analysis using the Bioconductor GenomicRanges R package. Perform interval operations, overlap analysis, windowed analysis, and genomic annotation. | Pipeline |
Picard1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| picard-toolkit | Picard Tools - High-Throughput Sequencing Processing | Comprehensive suite of Java-based command-line utilities for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Picard provides tools for data processing, quality control, metrics collection, and format conversion. | Pipeline |
Sequence Editing1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| sequence-editor-toolkit | Sequence Editor Toolkit | Edit, trim, translate, and manipulate DNA/RNA/protein sequences. Supports trimming, extracting regions, reverse complement, translation, transcription, quality filtering (FASTQ), masking, find/replace, and more. Intelligently chooses instant execution for small files (<5MB) or background processing for large files. | Sync |
Vcftools1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| vcftools-toolkit | VCFtools Toolkit | Comprehensive VCF/BCF file manipulation and analysis toolkit. Provides filtering, statistics, format conversion, merging, annotation, and quality control capabilities for variant call format files. | Pipeline |
File Reading1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| file-reader | File Reader - Read and Parse Data Files | Read and parse bioinformatics data files from workspace. Supports Word (.docx), Excel (.xlsx), CSV, PDF, FASTA (.fasta, .fa, .fna, .faa, .ffn, .frn, .fas, .fsa), and GenBank formats. Includes automatic OCR for scanned PDFs via AWS Textract. Provides multi-stage data intake: metadata only, structure preview, or full content. Use for reading experimental data, lab reports, protocols, understanding file structure, or extracting specific information. | Sync |
File Search1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| file-search | File Search - Discover Files in Workspace | Use this tool when the user asks to find, search, list, show, or discover files in their workspace (e.g., 'find files with...', 'show me files that contain...', 'what files have...'). Searches by name, content keywords, metadata, format, topics, sections, and tags. Returns file metadata without reading full content. Essential for file discovery before using file-reader. | Sync |
File Writer1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| file-writer | File Writer - Save Reports and Documents to Workspace | Save text content, reports, and documents as files in the user's workspace. Use after generating a report to save it as a markdown file that users can view and download. Supports plain text and markdown format. | Sync |
Gatk1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| gatk-toolkit | GATK Toolkit | Genome Analysis Toolkit (GATK) for variant discovery and genotyping in high-throughput sequencing data. Executes GATK tools on AWS infrastructure with automatic file management and process monitoring. | Pipeline |
Clinical Genomics1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| gwas-catalog | GWAS Catalog Disease Association Tools | Comprehensive plugin for NHGRI-EBI GWAS Catalog providing access to genome-wide association studies, SNP-trait associations, and disease genomics data | Sync |
Interpro1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| interpro-toolkit | InterPro Database Tools | Comprehensive plugin for InterPro protein functional analysis including domain prediction, family classification, and functional site identification | Sync |
Homer1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| homer-toolkit | HOMER - Hypergeometric Optimization of Motif EnRichment | Comprehensive suite for motif discovery, ChIP-Seq analysis, and peak annotation. Identifies enriched sequence motifs and analyzes transcription factor binding sites. | Pipeline |
Ncbi6 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ncbi-assembly | NCBI-Assembly | Search genome assembly information from NCBI Assembly database | Sync |
| ncbi-nucleotide | NCBI-Nucleotide | Search and retrieve nucleotide sequences (DNA/RNA) from NCBI Nucleotide database | Sync |
| ncbi-protein | NCBI-Protein | Search and retrieve protein sequences from NCBI Protein database | Sync |
| ncbi-sra | NCBI-SRA | Search Sequence Read Archive from NCBI SRA database | Sync |
| ncbi-structure | NCBI-Structure | Search protein structures from NCBI Structure database with PDB integration | Sync |
| ncbi-taxonomy | NCBI-Taxonomy | Search taxonomic information and organism classification from NCBI Taxonomy database | Sync |
Blast1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ncbi-blast | NCBI-BLAST | Perform sequence alignment and homology searches using NCBI BLAST | Pipeline |
Dbsnp1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ncbi-dbsnp | NCBI-dbSNP | Search SNP variant information from NCBI dbSNP database | Sync |
Literature1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ncbi-pubmed | NCBI-PubMed | Search PubMed literature database for scientific papers, articles, and reviews | Sync |
Drug Discovery1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| openfda-drug-toolkit | OpenFDA Drug Database Tools | Comprehensive drug information from FDA, EMA, and WHO databases including approvals, adverse events, labeling, and recalls | Sync |
Structural1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| pdb-toolkit | PDB Experimental Structure Database | Access experimentally determined protein structures from X-ray crystallography, NMR, and cryo-EM. Best for high-resolution experimental structures and validation data. Use AlphaFold for predicted structures. | Sync |
Pipeline3 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| list-pipelines | List Pipelines - Discover Predefined Bioinformatics Pipelines | List all available predefined bioinformatics pipelines. Returns pipeline names, descriptions, required inputs, and estimated duration. Use this BEFORE building a pipeline from scratch to check if a predefined pipeline already covers the user's need. Can filter by category (variant-calling, transcriptomics, genomics, epigenomics, quality-control, alignment, structural-biology). | Sync |
| pipeline-status | Pipeline Status - Check Multi-Step Pipeline Progress | Check the status and progress of a running multi-step bioinformatics pipeline. Returns overall pipeline status, individual step statuses, progress percentage, and output files when complete. Use after start-pipeline to monitor pipeline execution. | Sync |
| start-pipeline | Start Pipeline - Launch Multi-Step Bioinformatics Pipeline | Start a multi-step bioinformatics pipeline. Supports two modes: (1) pipelineId mode — pass a predefined pipeline id from list-pipelines and provide only the input parameters; the steps are loaded automatically from the registry. (2) Custom steps mode — provide an explicit steps[] array for one-off pipelines. Returns an executionId to track progress with pipeline-status tool. | Sync |
Process Management2 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| process-results | Process Results - Get Process Output Files | Retrieve output files and results from a completed bioinformatics process. Use when a process status shows 'completed' and you need to access the generated files (e.g., PDB structures, VCF variants, analysis reports). Returns file paths, URLs, or file content for downstream analysis. | Sync |
| process-status | Process Status - Check Running Process Status | Check the status of a long-running bioinformatics process by process ID. Use when the user asks 'is my process done?', 'what's the status of process X?', or wants to check if a process has completed. Returns process status (running, completed, failed, cancelled), progress, and error messages if applicable. | Sync |
Fastqc1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| fastqc-toolkit | FastQC - A quality control tool for high throughput sequence data | Quality control tool for high throughput sequencing data providing comprehensive quality assessment reports with summary graphs and statistics for raw sequence data. | Pipeline |
Fmlrc1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| fmlrc-toolkit | FMLRC - FM-index Long Read Error Correction | Long-read error correction tool using FM-index based methods to correct errors in noisy long reads using high-quality short reads as reference. | Pipeline |
Trimmomatic1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| trimmomatic-toolkit | Trimmomatic Toolkit | Comprehensive read trimming and adapter removal toolkit using Trimmomatic v0.39. Performs quality filtering, adapter trimming, and read preprocessing for both single-end and paired-end sequencing data. | Pipeline |
Samtools1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| samtools-toolkit | SAMtools Toolkit | Comprehensive SAM/BAM/CRAM file manipulation toolkit using SAMtools v1.13. Provides format conversion, indexing, statistics, editing, and viewing capabilities for sequencing alignment data. | Pipeline |
Protein1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| smartsmatch-protein | SmartMatch Protein Search | Fast protein similarity search using AI-powered vector embeddings. Find similar proteins by sequence with subsecond response times. Alternative to BLAST for rapid protein identification. | Pipeline |
Tabix1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| tabix-query | Tabix Query | Fast indexed genomic file queries using Tabix/TBI indexes. Query specific regions from compressed VCF, BED, GFF files without full extraction. Runs locally with HTTP range request support for efficient S3 access. | Sync |
Web1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| tavily-search | Tavily Web Search | Search the web for scientific literature and bioinformatics information using Tavily API | Sync |
Ucsc1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| ucsc-genome-browser | UCSC Genome Browser | Access genome annotation and visualization data from the UCSC Genome Browser database | Sync |
Patents1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| uspto-patents-search | USPTO Patents Search | Search US patent database via PatentsView API for intellectual property research and prior art analysis | Sync |
Visualization1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| visualization-generator | Visualization Generator - Create Charts and Plots | Generate professional charts, plots, and diagrams for scientific reports. Supports standard charts (bar, line, scatter, pie), specialized bioinformatics plots (volcano, MA, Manhattan, heatmap), workflow diagrams, and 3D molecular structures. Visualizations are saved to workspace and can be included in reports. | Sync |
Compression1 tools
| Tool ID | Name | Description | Mode |
|---|---|---|---|
| zip-toolkit | Zip Toolkit | Comprehensive file compression and decompression toolkit supporting ZIP, GZIP, BZIP2, XZ, 7-Zip, and TAR formats. Handles bioinformatics files that are commonly distributed in compressed formats. | Pipeline |
Looking for predefined pipelines? Multi-step bioinformatics workflows (WES alignment, RNA-seq, GATK variant calling, protein binder design, and more) are documented on the Predefined Pipelines page.
Fetch the Tool List at Runtime
Call GET /v1/tools to retrieve the live tool registry with each tool's ID, parameter schema, and description.
from smartsbio import SmartsBio
client = SmartsBio(api_key="sk_live_...")
tools = client.tools.list()
for tool in tools:
print(f"{tool.id:40s} [{tool.category}]")
# Filter by category
protein_design = [t for t in tools if t.category == "AI Protein Design"]
pipeline_tools = [t for t in tools if t.invocation in ("pipeline", "both")]
# Inspect a tool's parameter schema
blast = next(t for t in tools if t.id == "ncbi_blast")
for param in blast.parameters:
print(f" {param.name} ({'required' if param.required else 'optional'}): {param.description}")Run a Tool Directly
# Sync tool — results returned immediately
result = client.tools.run(
tool_id="ncbi_pubmed",
input={"query": "BRCA1 breast cancer 2024", "maxResults": 5},
)
for article in result["results"]:
print(f"{article['pmid']}: {article['title']}")
# Pipeline tool — submit and poll
pipeline = client.pipelines.create(
tool_id="protein_structure_prediction",
workspace_id=ws_id,
input={"sequence": "MKTIIALSYIFCLVFA...", "model": "boltz2"},
)
pipeline = client.pipelines.wait(pipeline["id"], workspace_id=ws_id,
on_progress=lambda p: print(p["progress_pct"], "%"))
client.files.download(pipeline["output_keys"][0], workspace_id=ws_id, dest="./structure.pdb")