RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching

TL;DR

RNACG is a versatile RNA sequence generation framework that uses flow matching to incorporate various structural, functional, and family annotations, enabling customizable and unified RNA design.

Contribution

It introduces RNACG, a universal, modular RNA sequence generator based on flow matching that supports diverse conditional inputs and design paradigms.

Findings

Supports multiple annotation types for RNA design

Unifies various RNA design tasks in a single framework

Enables customizable encoding networks

Abstract

RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of functional sequences. However, RNA design remains challenging due to the inherent flexibility of RNA molecules and the scarcity of experimental data on tertiary and secondary structures compared to proteins. These limitations highlight the need for a more universal and comprehensive approach to RNA design that integrates diverse annotation information at the sequence level. To address these challenges, we propose RNACG (RNA Conditional Generator), a universal framework for RNA sequence design based on flow matching. RNACG supports diverse conditional inputs, including structural, functional, and family-specific annotations, and offers a modular design that allows users to customize the encoding network for specific tasks. By unifying sequence generation under a single framework, RNACG enables the integration of multiple RNA design paradigms, from family-specific generation to tertiary structure inverse folding.