Tamarind Bio

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 order. Not for computational prediction or compute jobs.

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, fixed-backbone inverse folding, docking an existing ligand, or predicting an existing structure.

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 onto Tamarind so it can be submitted like a built-in tool. Not for running a tool that already exists in the Tamarind catalog, and not for choosing among built-in tools.

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 for generating molecules, folding structures, or measuring binding alone.

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 prediction.

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, or running a model from listFinetunedModels. Not for stock inference or custom training code.

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, or ordinary folding.

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 dedicated Tamarind MCP skill.

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 stages depend on earlier stages (design to fold to score), or to run or re-run a saved pipeline template. Not for a single job, one independent batch, or CLI orchestration.

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.