tamarind-cli

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

Skills (16)

• tamarind-antibody

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

• tamarind-api-setup

  Install, upgrade, authenticate, or troubleshoot the Tamarind CLI before running Tamarind Bio jobs. Use when `tamarind` is missing or incompatible, authentication is absent or rejected, endpoints/profiles need configuration, or a safe no-spend connectivity check is needed. Not for submitting compute

• tamarind-batch

  Run one Tamarind Bio tool across many independent inputs as a tracked batch, then monitor the parent, inspect subjobs, download aggregation, and rank completed results. Use for libraries and screens. Not for one input, multiple dependent tool stages, or an unbounded loop of individual submissions.

• tamarind-binder-design

  Design new de novo protein, peptide, macrocycle, or small-molecule binders against a target with Tamarind Bio, then refold and rank candidates. Use for backbone/sequence or ligand generation from scratch. Not for antibody-specific CDR engineering, fixed-backbone inverse folding, docking an existing

• tamarind-custom-tool-deploy

  Convert a local folder or git repository into the Tamarind Custom Tool format and deploy it through the unified Tamarind CLI. Use when onboarding a model, script, or container so an organization can submit it like a built-in tool. Not for running an existing catalog tool or configuring GitHub push-t

• tamarind-developability

  Score protein or antibody candidates for manufacturability and clinic-readiness with Tamarind Bio, including stability, aggregation, solubility, viscosity, polyreactivity, glycosylation, and immunogenicity. Use as a post-design filter. Not for generating molecules, folding structures, or measuring b

• tamarind-docking

  Dock or screen known ligands against a receptor, perform protein-protein docking, or score binding affinity/interface quality from existing structures with Tamarind Bio. Use for pocket-based or blind docking and pose ranking. Not for co-folding from sequence, generating a new ligand or binder, or ge

• tamarind-finetune

  Fine-tune a Tamarind-hosted model on user-provided labeled data and run the matching inference tool with the trained job. Use for supported finetune/inference pairs in protein, affinity, enzyme, or small-molecule workflows. Not for stock pretrained inference, ordinary batch prediction, or unsupporte

• tamarind-inverse-folding

  Design sequences for a fixed protein backbone or run protein language models for embeddings, mutation scoring, and sequence generation with Tamarind Bio. Use for ProteinMPNN-, LigandMPNN-, ESM-IF-, or PLM-style tasks. Not for de novo backbone generation, antibody CDR design, or ordinary structure pr

• tamarind-miniprotein-campaign

  Run Anthropic's published de novo miniprotein binder campaign protocol with Tamarind Bio 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 mo

• tamarind-more-tools

  Discover and run Tamarind Bio tools outside the dedicated protein-folding, binder, antibody, docking, inverse-folding, and developability skills. Use for enzyme work, small-molecule properties/QM, molecular dynamics, nucleic acids, cryo-EM, structure search, and format utilities. Not for a domain th

• tamarind-pipeline

  Orchestrate multiple dependent Tamarind Bio tools as a resumable CLI campaign where each successful stage feeds the next, such as design to fold to score. Use when later stages depend on earlier artifacts or metrics. Not for one job or one tool applied independently across many inputs.

• tamarind-results-analysis

  Recover and analyze an existing Tamarind Bio job by name: check or wait for status, inspect logs and metrics, download results, rank scientific outputs, and prepare a downstream input. Use after submission, across sessions, or when a previous command was interrupted. Not for starting a new job or ch

• tamarind-structure-prediction

  Predict or co-fold a protein, peptide, nucleic acid, ligand, or biomolecular complex from sequence with Tamarind Bio. Use for AlphaFold-, Boltz-, Chai-, ESMFold-, or Protenix-style structure prediction and confidence interpretation. Not for de novo binder generation, fixed-backbone sequence design,

• tamarind-submit-and-poll

  Run one known Tamarind Bio tool end to end through the Tamarind CLI: validate settings, confirm consequential choices and spend, submit once, wait with a timeout, inspect terminal status, and download results. Also use to reattach to one already-submitted job. Not for tool selection, batch submissio

• tamarind-tool-discovery

  Choose which Tamarind Bio tool fits a scientific goal by querying the live CLI catalog and schema. Use when the user has not named a tool, when several tools could fit, or when availability and required inputs must be verified. Not for installing/authenticating the CLI or executing a tool that is al

Similar plugins