Secondary Structure

Secondary structure prediction, focusing on the 3D arrangement of biomolecules like proteins and RNA, aims to determine these structures from their primary sequences. Current research heavily utilizes deep learning approaches, including convolutional neural networks (CNNs) with large kernels and transformer-based architectures, to predict secondary structures with improved accuracy, particularly for complex structures like pseudoknots. These advancements are significantly impacting fields like synthetic biology and drug design by enabling the generation of novel proteins and nucleic acids with desired properties, and improving our understanding of complex biological processes through enhanced visualization techniques. The development of more accurate and efficient prediction methods continues to be a major focus.

Papers

July 15, 2024

OmniGenome: Aligning RNA Sequences with Secondary Structures in Genomic Foundation Models
Heng Yang, Ke Li
Foundation Model RNA Sequence RNA Design Sequence Alignment Secondary Structure

June 4, 2024

Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction
Marc Harary, Chengxin Zhang
RNA Structure Secondary Structure

May 30, 2024

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation
Guillaume Huguet, James Vuckovic, Kilian Fatras, Eric Thibodeau-Laufer, Pablo Lemos, Riashat Islam, Cheng-Hao Liu, Jarrid Rector-Brooks, Tara Akhound-Sadegh, Michael Bronstein, Alexander Tong, Avishek Joey Bose
Flow Matching Protein Backbone Generation Secondary Structure FoldFlow 2

November 6, 2023

ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings
Chenwei Zhang, Jordan Lovrod, Boyan Beronov, Khanh Dao Duc, Anne Condon
Secondary Structure DNA Hybridization

May 7, 2023

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins
Markus J. Buehler
Generative Model General Analysis Scientific Discovery Pre Trained Generative Model Protein Design Protein Model Secondary Structure

August 24, 2022

Secondary Protein Structure Prediction Using Neural Networks
Sidharth Malhotra, Robin Walters
Neural Network Protein Sequence Amino Acid Neural Network Structure Secondary Structure

Secondary Structure

Papers

OmniGenome: Aligning RNA Sequences with Secondary Structures in Genomic Foundation Models

Kirigami: large convolutional kernels improve deep learning-based RNA secondary structure prediction

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation

ViDa: Visualizing DNA hybridization trajectories with biophysics-informed deep graph embeddings

Generative Pretrained Autoregressive Transformer Graph Neural Network applied to the Analysis and Discovery of Novel Proteins

Secondary Protein Structure Prediction Using Neural Networks