Proto is a universal framework for AI-driven biological design that enables programmable generation across DNA, RNA, proteins, ligands, and their interactions. Proto abstracts biological design into four primitives—sequences, generators, constraints, and optimizers—allowing users to specify high-level functional objectives and compose diverse AI models into unified design workflows. By compiling user-defined constraints into a shared optimization objective, Proto supports multi-modal, multi-objective design to generate de novo biological sequences that satisfy complex functional requirements. A Python library for local runs, a hosted cloud API, a drag-and-drop graphical interface, and AI-agent-compatible programming framework make generative biology accessible to both experimental and computational biologists.

Github

Proto on Github