RNA Structure
Understanding RNA structure through sequence, topology, evolutionary constraints, and physical principles.
TriRNASP · tpFormer
Personal research / Computational RNA
Tovi Yuan.
RNA Structure · Design · AI
Computational modeling, physical principles, and artificial intelligence for understanding and designing RNA.
Connecting structural statistics, topology, and evolutionary information with the question of how RNA folds—and how it might be designed.
01Research interests
Research overview ↗RNA Design
Designing sequences for desired three-dimensional structures, with function as a longer-term question.
DS3dRNA
Computational Biophysics
Using structural statistics and physical models to study molecular organization and structural scoring.
TriRNASP · DS3dRNA
AI for Molecular Science
Exploring models that connect structural, topological, evolutionary, and physical information.
tpFormer · Future directions
02Featured projects
All projects ↗01Active research
RNA structure
tpFormer
Topology-aware RNA structure modeling that brings sequence, contacts, and evolutionary information into iterative refinement.
02Public software
RNA 3D design
DS3dRNA
De novo sequence design for target RNA 3D structures, using structural constraints and higher-order interactions.
03Published work
RNA structure evaluation
TriRNASP
RNA structural scoring with a knowledge-based potential that incorporates three-body structural information.
03Selected publication
Publication index ↗- 2026Published
TriRNASP: A knowledge-based potential with three-body effects for accurate RNA structure evaluation
Biophysical Journal 125(11), 2526–2540
04A landscape of ideas
Connected ideas across current work and future questions.
Size indicates conceptual emphasis. Groups identify research status.
Core focus
- RNA
Published work
- RNA Structure
- Computational Biophysics
- RNA 3D Structure
- Statistical Potentials
- Three-body Interactions
- Structural Biology
- Tertiary Structure
Active projects
- RNA Design
- Topology-aware Learning
- Evolution
- MSA
- Machine Learning
- Structure Prediction
- Contact Map
- Topology
- de novo Design
- Secondary Structure
- Deep Learning
Exploratory interests
- Synthetic Biology
- RNA Foundation Models
- Energy Landscape
- Functional RNA
- Geometric Learning
- Physics-informed AI
- Ribozyme
- RNA Engineering
- Molecular Design
Current directions
From structural principles
to molecular design.
Topology-aware RNA modeling and evolutionary information guide current questions in structure prediction. Longer-term interests include RNA foundation models, de novo design, and AI-guided RNA engineering grounded in physical and statistical potentials.
Explore research directions →