Agents
10+ built-in agents. 50+ tools. Boltz, ProteinMPNN, Smina, AutoDock Vina, APBS, and more, packaged into one platform for prediction, docking, electrostatics, antibody design, and de novo binders.
What they do
Each agent ships with the right package stack for one domain, including GPU-backed prediction and design where it matters. It can run fully agentic or as a fixed execution path, and it can plug into larger orchestrators when a workflow crosses domains.
Each agent ships with the package stack that fits one job. Boltz and docking engines for prediction. ProteinMPNN for sequence design. APBS for electrostatics. Antibody tools for developability. The right tools are obvious before you even start.
Two run modes. Agentic lets a reasoning model like Claude Opus pick tools and chain them together. Fixed-run executes a known path from defined inputs to defined outputs, with no reasoning tax. Pick whichever fits the science and the budget.
Bring your own agents, your own tools, or your own orchestrator. Let MARA or your own reasoning layer coordinate specialized sub-agents across protein, small-molecule, and antibody work.
The agents
From Boltz-powered prediction and docking to ProteinMPNN, APBS, and antibody analysis, each agent wraps the right package stack in a scientist-facing product.
Run protein prediction, co-folding, and docking across Boltz-2, Smina, AutoDock Vina, and more. Automatic file conversion, pocket detection, and job setup included.
Set up watched folders that auto-trigger prediction and docking jobs when new molecules arrive. Chain with other agents for closed-loop pipelines.
Protein sequence design with ProteinMPNN. Fix the residues that matter, redesign the rest, then run it as a fixed pipeline or in AI reasoning mode.
Design protein binders from scratch with iterative prediction, scoring, and refinement. Results ship to MARA for 3D review.
Full APBS electrostatics in one packaged flow, from protonation through complementarity analysis. Every stage in its own tab.
End-to-end antibody design: sequence analysis, structure prediction, developability, and optional ADC design in one packaged flow.
Break a matched series into core + R-group tables to map SAR across analogs. Pairs with MMP transforms and auto-docking for closed-loop analog design.
Standalone CDR mapping, humanization scoring, developability checks, and ADC design when you need the antibody package stack without the full workflow.
Individual electrostatic steps (molecule prep, pdb2pqr, APBS, DX analysis) for when you need one stage without the full workflow.
Build your own
Bring your own agents, your own tools, and your own orchestrator patterns. Extend the built-ins, or let MARA and your own reasoning layer coordinate specialized agents across protein, small-molecule, and antibody work. The platform is open for your group's workflows, not just ours.