Speak to a Protein: An Interactive Multimodal Co-Scientist for Protein Analysis

Abstract

Abstract Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires specialized computational skills. We introduce Speak to a Protein, a new capability that turns protein analysis into an interactive, multimodal dialogue with an expert coscientist. The AI system retrieves and synthesizes relevant literature, structures, and ligand data; grounds answers in a live 3D scene; and can highlight, annotate, manipulate, and see the visualization. It also generates and runs code when needed, explaining results in both text and graphics. We demonstrate these capabilities on relevant proteins, posing questions about binding pockets, conformational changes, or structure-activity relationships to test ideas in real time. Speak to a Protein reduces the time from question to evidence, lowers the barrier to advanced structural analysis, and enables hypothesis generation by tightly coupling language, code, and 3D structures. Speak to a Protein is freely accessible at https://open.playmolecule.org.

The authors' abstract, as published at the source. Journal of Chemical Information and Modeling, 2026 · DOI ↗