Proteo-R1: Reasoning Foundation Models for De Novo Protein Design
Authors: Fang Wu, Weihao Xuan, Heli Qi, Hanqun CAO, Heng-Jui Chang, Heng-Jui Chang, Zeqi Zhou, Haokai Zhao, Ma Jian, Jian Ma, Carl Ma, Zijian Carl Ma, Yu-Chi Cheng, Yu-Chi Cheng, Kuan Pang, Xiangru Tang, Zehong Wang, Guanlue Li, Hanchen Wang, Kejun Ying, Pan Lu, Chiho Im, Seungju Han, Peng Xia, Tinson Xu, Yinxi Li, Deyao Zhu, Pheng-Ann Heng, Pheng-Ann Heng, Naoto Yokoya, Masashi Sugiyama, Li Erran Li, Jure Leskovec, Yejin Choi
Abstract
Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce Proteo-R1, a reasoning-guided protein design framework that explicitly decouples molecular understanding from geometric generation. Proteo-R1 adopts a dual-expert architecture, where a multimodal large language model (LLM) serves as an understanding expert, analyzes protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed to a separate diffusion-based generation expert, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with advanced geometric generative models. Code and demos are at https://proteor1.github.io.