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-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. 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-developability

Score protein or antibody candidates for stability, aggregation, solubility, viscosity, polyreactivity, glycosylation, immunogenicity, and related developability risks with Tamarind Bio through MCP. 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 a supported Tamarind-hosted model on labeled data and run its matching inference tool through MCP. Use for live account-visible finetune/inference pairs in protein, affinity, enzyme, or small-molecule workflows. Not for stock inference, ordinary batch prediction, or unsupported 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

Orchestrate multiple dependent Tamarind Bio tools as a resumable MCP campaign where successful stages feed later stages, such as design to fold to score. Use when stages depend on earlier artifacts or metrics. Not for one job, one independent batch, a nonexistent submitPipeline call, 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.

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 docking into a known pocket.