Protein and molecular design
Connect your AI to your Tamarind Bio workspace for protein and molecular science. Browse, validate, estimate, submit, and monitor work across 300+ tools for structure prediction, docking, protein and antibody design, molecular dynamics, and property prediction. More
What you can ask Run a miniprotein binder design pipeline against PD-L1, monitor it, and rank the best candidates. Copy
Example path getPipelineRun Tamarind MCP Binder Design skill
Create a molecule group from these SMILES, search related molecules, and dock the best candidates into ABL1. Deploy a custom analysis tool from my repository and use it in a reproducible pipeline. MCP connector Server URL https://mcp.tamarind.bio/mcpCopy Login OAuth Tools Reads data31 estimateTime getAvailableModels getAvailableTools getCustomTool getFiles getFileStats getFolders getJobFile getJobLogs getJobs getJobSchema getMoleculeImport getPipelineRun getPipelineRunResults getPipelineSchema getPipelineTemplate getResult listAssays listAssayTargets listAssayTypes listFinetunedModels listJobFiles listModalities listMoleculeGroups listPipelineRuns listPipelineTemplates listProjects listTags searchMolecules validateJob validatePipeline
Changes data7 createProject importMoleculeFile submitAssay submitBatch submitFinetuningRun submitJob submitPipeline
Deletes or can't be undone9 cancelAssay cancelBatch cancelJob createMolecules deleteFile deleteJob deployCustomTool stopPipelineRun uploadFile
Skills 16 in the ChatGPT listing
Tamarind MCP Antibody Design, redesign, model, number, humanize, or search antibodies, nanobodies, VHHs, and TCRs with Tamarind Bio through MCP. Tamarind MCP Wet-Lab Assays Order wet-lab assays of designed sequences from Tamarind's partner labs (Adaptyv, Ginkgo, A-Alpha Bio) through MCP for clearly benign research, diagnostic, or therapeutic development, then track or cancel the order and download results. Tamarind MCP Batch Run one Tamarind Bio tool across many independent inputs with one MCP submitBatch call, then monitor subjobs and rank completed results. Tamarind MCP Binder Design Design new protein, peptide, macrocycle, or small-molecule binders against a target with Tamarind Bio through MCP, then refold and rank candidates for clearly benign research, diagnostic, or therapeutic discovery. Tamarind MCP Custom Tool Deploy Convert a local folder or a git repository into the Tamarind custom-tool format and deploy it as an organization tool through MCP - author Dockerfile, run.sh, and config.json, build a numbered version, poll it, publish it, then smoke-test. Tamarind MCP Developability Score protein or antibody candidates for stability, aggregation, solubility, viscosity, polyreactivity, glycosylation, immunogenicity, and related developability risks with Tamarind Bio through MCP for clearly benign research, diagnostic, or therapeutic development. Tamarind MCP Docking Dock or screen known ligands against a receptor, perform protein-protein docking, or score existing poses and complexes with Tamarind Bio through MCP. Tamarind MCP Fine-tuning Fine-tune (train) a Tamarind-hosted model on the user's labeled data with submitFinetuningRun, then run it by modelId through MCP, for clearly benign research, diagnostic, or therapeutic development. Tamarind MCP Inverse Folding Design sequences for a fixed protein backbone or run protein language models for embeddings, mutation scoring, likelihoods, and sequence generation with Tamarind Bio through MCP. Tamarind MCP More Tools Discover and run Tamarind Bio tools outside the dedicated MCP structure, binder, antibody, docking, inverse-folding, and developability skills. Tamarind MCP Pipeline Author, validate, run, monitor, and read results from declarative multi-step Tamarind Bio pipelines through MCP with submitPipeline, validatePipeline, getPipelineSchema, getPipelineTemplate, listPipelineTemplates, getPipelineRun, getPipelineRunResults, listPipelineRuns, and stopPipelineRun. Tamarind MCP Results Recover and analyze an existing Tamarind Bio job or batch through MCP by durable name, including bounded monitoring, logs, metrics, output-file inspection, cancellation, and downstream artifact selection. Tamarind MCP Setup Connect, authenticate, or troubleshoot the Tamarind Bio MCP server and run a no-spend connectivity check. Tamarind MCP Structure Prediction Predict or co-fold proteins, peptides, nucleic acids, ligands, or biomolecular complexes with Tamarind Bio through MCP. Tamarind MCP Job Runner Run one known Tamarind Bio tool end to end through MCP by validating settings, estimating runtime and weighted hours, confirming consequential choices, submitting once, polling with a finite deadline, and retrieving results. Tamarind MCP Tool Discovery Choose a Tamarind Bio tool by querying the live MCP catalog and schema. 
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