Scientific discovery games for biomedical research

R Das, B Keep, P Washington… - Annual review of …, 2019 - annualreviews.org
Over the past decade, scientific discovery games (SDGs) have emerged as a viable
approach for biomedical research, engaging hundreds of thousands of volunteer players …

RNA design via structure-aware multifrontier ensemble optimization

T Zhou, N Dai, S Li, M Ward, DH Mathews… - …, 2023 - academic.oup.com
Motivation RNA design is the search for a sequence or set of sequences that will fold to
desired structure, also known as the inverse problem of RNA folding. However, the …

gRNAde: Geometric Deep Learning for 3D RNA inverse design

CK Joshi, AR Jamasb, R Viñas, C Harris, S Mathis… - …, 2024 - pmc.ncbi.nlm.nih.gov
Computational RNA design tasks are often posed as inverse problems, where sequences
are designed based on adopting a single desired secondary structure without considering …

Fitness functions for RNA structure design

M Ward, E Courtney, E Rivas - Nucleic Acids Research, 2023 - academic.oup.com
An RNA design algorithm takes a target RNA structure and finds a sequence that folds into
that structure. This is fundamentally important for engineering therapeutics using RNA …

Rnaformer: A simple yet effective deep learning model for rna secondary structure prediction

JKH Franke, F Runge, R Köksal, R Backofen, F Hutter - bioRxiv, 2024 - biorxiv.org
Traditional RNA secondary structure prediction methods, based on dynamic programming,
often fall short in accuracy. Recent advances in deep learning have aimed to address this …

Community science designed ribosomes with beneficial phenotypes

A Krüger, AM Watkins, R Wellington-Oguri… - Nature …, 2023 - nature.com
Functional design of ribosomes with mutant ribosomal RNA (rRNA) can expand
opportunities for understanding molecular translation, building cells from the bottom-up, and …

An unexpectedly effective Monte Carlo technique for the RNA inverse folding problem

F Portela - BioRxiv, 2018 - biorxiv.org
Solving the RNA inverse folding problem, also known as the RNA design problem, is critical
to advance several scientific fields like bioengineering, yet existing approaches have had …

RnaBench: A Comprehensive Library for In Silico RNA Modelling

F Runge, K Farid, JKH Franke, F Hutter - bioRxiv, 2024 - biorxiv.org
ABSTRACT RNA is a crucial regulator in living organisms and malfunctions can lead to
severe diseases. To explore RNA-based therapeutics and applications, computational …

A QUBO model of the RNA folding problem optimized by variational hybrid quantum annealing

T Zaborniak, J Giraldo, H Müller… - 2022 IEEE …, 2022 - ieeexplore.ieee.org
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into
specific, stable structures that substantially govern their biochemical behaviour …

EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame

RV Koodli, B Keep, KR Coppess, F Portela… - PLoS computational …, 2019 - journals.plos.org
Emerging RNA-based approaches to disease detection and gene therapy require RNA
sequences that fold into specific base-pairing patterns, but computational algorithms …