Submits and manages FastFold protein folding jobs via the Jobs API (Boltz-2, OpenFold 3, Chai-1, IntelliFold, ESMFold2, Nesso-1, AlphaFold2, SimpleFold). Covers authentication, job payloads, modifications, constraints, webhooks (Evolla, OpenMM, Nesso affinity…
Run molecular dynamics (MD) simulations via the FastFold Workflows API. Today supports the CALVADOS+OpenMM workflow (calvados_openmm_v1) from either an existing fold job (AF structure + PAE auto-resolved) or manual PDB+PAE upload, then waits for completion,…
Run OpenMMDL molecular dynamics workflows via the FastFold Workflows API (`openmmdl_v1`) from local topology + optional ligand files, prepare draft scripts, execute drafts, wait for completion, fetch artifacts/metrics, and extract trajectory frames. Use when…
Build and run FastFold BoltzGen protein-design workflows end-to-end through API or Composer draft links. Use this whenever users mention BoltzGen, design-spec YAMLs, binder design, multi-spec scaffold workflows, CIF/PDB preparation, workflow graph upsert,…
Run Boltz API workflows via the official `boltz-api` CLI — structure-and-binding, protein design/screen, small-molecule design/screen, ADME prediction, and job status/recovery. Use when the user wants to estimate, submit, monitor, fetch results for, stop, or…
Share markdown reports to the user's configured Slack agent_cli_report channel via Fastfold API, and persist the markdown as a library item.
Generate Mermaid diagrams on demand and proactively for complex multi-step workflows. Use when users ask for flowcharts/diagrams, or when explaining complicated pipelines such as BoltzGen, fold->MD, and computational biology execution flows.