13 citations · 31 across the 8 of their papers we have counts for
8 papers
Machine learning for RNA-targeting drug design
Wissam Karroucha, Carlos Oliver, Veronique Stoven +1
Targeting RNA with small molecules offers significant therapeutic potential. Machine learning could substantially accelerate preclinical drug discovery, from hit identification to…
BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction
Xin Wang, Kaiwen Shi, Carlos Oliver
Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Y…
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling
Luis Wyss, Vincent Mallet, Wissam Karroucha +2
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure mode…
3D-based RNA function prediction tools in rnaglib
Carlos Oliver, Vincent Mallet, Jérôme Waldispühl
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, build…
Edge-similarity-aware Graph Neural Networks
Vincent Mallet, Carlos G. Oliver, William L. Hamilton
Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\texti…
RNAglib: A Python Package for RNA 2.5D Graphs
Vincent Mallet, Carlos Oliver, Jonathan Broadbent +2
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficientl…
VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs
Carlos Oliver, Vincent Mallet, Pericles Philippopoulos +2
RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automat…
Leveraging binding-site structure for drug discovery with point-cloud methods
Vincent Mallet, Carlos G. Oliver, Nicolas Moitessier +1
Computational drug discovery strategies can be broadly placed in two categories: ligand-based methods which identify novel molecules by similarity with known ligands, and structure…