Cover Image

A Comprehensive Benchmark for RNA 3D Structure-Function Modeling

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Wyss, Luis, Mallet, Vincent, Karroucha, Wissam, Borgwardt, Karsten, Oliver, Carlos
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Machine learning for RNA-targeting drug design
by: Karroucha, Wissam, et al.
Published: (2025)

3D-based RNA function prediction tools in rnaglib
by: Oliver, Carlos, et al.
Published: (2024)

Endowing Protein Language Models with Structural Knowledge
by: Chen, Dexiong, et al.
Published: (2024)

Protein Fold Classification at Scale: Benchmarking and Pretraining
by: Chen, Dexiong, et al.
Published: (2026)

AtomSurf : Surface Representation for Learning on Protein Structures
by: Mallet, Vincent, et al.
Published: (2023)

NbBench: Benchmarking Language Models for Comprehensive Nanobody Tasks
by: Zhang, Yiming, et al.
Published: (2025)

Rethinking Performance Measures of RNA Secondary Structure Problems
by: Runge, Frederic, et al.
Published: (2023)

A Comparative Review of RNA Language Models
by: Wang, He, et al.
Published: (2025)

RiNALMo: General-Purpose RNA Language Models Can Generalize Well on Structure Prediction Tasks
by: Penić, Rafael Josip, et al.
Published: (2024)

RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design
by: Anand, Rishabh, et al.
Published: (2024)

α-HMM: A Graphical Model for RNA Folding
by: Zhang, Sixiang, et al.
Published: (2024)

CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction
by: Han, Rong, et al.
Published: (2024)

Machine Learning Modeling Of SiRNA Structure-Potency Relationship With Applications Against Sars-Cov-2 Spike Gene
by: Oshunyinka, Damilola
Published: (2024)

RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
by: Rubin, Dana, et al.
Published: (2025)

ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings
by: Hanke, Josef, et al.
Published: (2026)

RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching
by: Nori, Divya, et al.
Published: (2024)

Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
by: Gao, Kaiyuan, et al.
Published: (2024)

DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions
by: Zeng, Xinyue, et al.
Published: (2025)

Compact Artificial Neural Network Models for Predicting Protein Residue -- RNA Base Binding
by: Selitskiy, Stanislav
Published: (2025)

Generative molecule evolution using 3D pharmacophore for efficient Structure-Based Drug Design
by: He, Yi, et al.
Published: (2025)

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling
by: Yang, Yuwei, et al.
Published: (2024)

Comprehensive benchmarking of large language models for RNA secondary structure prediction
by: Zablocki, L. I., et al.
Published: (2024)

COMET: Benchmark for Comprehensive Biological Multi-omics Evaluation Tasks and Language Models
by: Ren, Yuchen, et al.
Published: (2024)

Benchmarking Large Language Models for Molecule Prediction Tasks
by: Zhong, Zhiqiang, et al.
Published: (2024)

RNA Secondary Structure Prediction Using Transformer-Based Deep Learning Models
by: Zhou, Yanlin, et al.
Published: (2024)

Learning Protein Structure-Function Relationships through Knowledge-guided Representation Decomposition
by: Wang, Mingqing, et al.
Published: (2026)

RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching
by: Gao, Letian, et al.
Published: (2024)

gRNAde: Geometric Deep Learning for 3D RNA inverse design
by: Joshi, Chaitanya K., et al.
Published: (2023)

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
by: Lu, Shuqi, et al.
Published: (2025)

3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information
by: Kuang, Taojie, et al.
Published: (2023)

Structure-Informed Protein Language Model
by: Zhang, Zuobai, et al.
Published: (2024)

Molecular Fingerprints Are Strong Models for Peptide Function Prediction
by: Adamczyk, Jakub, et al.
Published: (2025)

Structure Language Models for Protein Conformation Generation
by: Lu, Jiarui, et al.
Published: (2024)

Insights Into the Inner Workings of Transformer Models for Protein Function Prediction
by: Wenzel, Markus, et al.
Published: (2023)

Messenger RNA Design via Expected Partition Function and Continuous Optimization
by: Dai, Ning, et al.
Published: (2023)

UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design
by: Kong, Xiangzhe, et al.
Published: (2025)

Structure-based Drug Design with Equivariant Diffusion Models
by: Schneuing, Arne, et al.
Published: (2022)

Function-Guided Conditional Generation Using Protein Language Models with Adapters
by: Yang, Jason, et al.
Published: (2024)

Open-Source Protein Language Models for Function Prediction and Protein Design
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)

A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design
by: Gharbi, Yossra, et al.
Published: (2024)