tamarind-mcp

Plugin tamarind-mcp from marketplace tamarind-agent-plugin in Tamarind-Bio/tamarind-agent-plugin. Commands read from the repo's manifest — 9 days ago.

Skills (17)

• tamarind-mcp-antibody

  Design, redesign, model, number, humanize, or search antibodies, nanobodies, VHHs, and TCRs with Tamarind Bio through MCP. Use for CDR-aware and repertoire-specific workflows when MCP is requested. Not for generic non-antibody binder design, ordinary complex folding, or developability scoring alone.

• tamarind-mcp-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. Use for real lab measurements, their price, or an existing orde

• tamarind-mcp-batch

  Run one Tamarind Bio tool across many independent inputs with one MCP submitBatch call, then monitor subjobs and rank completed results. Use for libraries, screens, generated-sequence refolding, or repeated inference. Not for one input, dependent tool stages, loops of submitJob, or CLI batches.

• 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. Use for de novo generation when MCP is requested. Not for antibody CDR engineering, fi

• 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. Use when onboarding your own model, script, or container ont

• 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. Use as a post-design filter. Not

• 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. Use for pocket-based or blind docking and pose ranking. Not for sequence co-folding, generating a new ligand or binder, or general structure predicti

• tamarind-mcp-finetune

  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. Use for training or retraining a property, affinity, fitness, or enzyme predictor, a training sweep,

• 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. Use for ProteinMPNN-, LigandMPNN-, ESM-IF-, or PLM-style tasks. Not for de novo backbone generation, antibody CDR design,

• tamarind-mcp-miniprotein-campaign

  Run Anthropic's published de novo miniprotein binder campaign protocol through Tamarind MCP against one target and epitope — multi-method generation under a per-method floor, four pre-scoring gates, a three-arm co-folding instrument frozen and control-validated before any production scoring, five or

• tamarind-mcp-more-tools

  Discover and run Tamarind Bio tools outside the dedicated MCP structure, binder, antibody, docking, inverse-folding, and developability skills. Use for enzymes, small-molecule properties or QM, molecular dynamics, nucleic acids, cryo-EM, structure search, and utilities. Not for a domain with a dedic

• 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. Use when

• tamarind-mcp-results-analysis

  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. Use after submission or across sessions. Not for starting a new job or using the CLI.

• tamarind-mcp-setup

  Connect, authenticate, or troubleshoot the Tamarind Bio MCP server and run a no-spend connectivity check. Use when Tamarind MCP tools are missing, OAuth is incomplete or rejected, or the user wants MCP rather than the Tamarind CLI. Not for selecting a scientific model or submitting compute.

• tamarind-mcp-structure-prediction

  Predict or co-fold proteins, peptides, nucleic acids, ligands, or biomolecular complexes with Tamarind Bio through MCP. Use for live AlphaFold-, Boltz-, Chai-, ESMFold-, or Protenix-style structure workflows when MCP is requested. Not for de novo binder generation, antibody-specific modeling, or doc

• tamarind-mcp-submit-and-poll

  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. Also use to reattach to one existing job. Not for tool selection, batch sub

• tamarind-mcp-tool-discovery

  Choose a Tamarind Bio tool by querying the live MCP catalog and schema. Use when the user requests MCP, has not named a tool, several tools could fit, or availability and required inputs must be verified. Not for reconnecting OAuth or executing a tool that is already selected.

MCP servers (1)

• tamarind

  connects to: https://mcp.tamarind.bio/mcp

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