Vincent Mallet

Publications

Article dans une revue (9)

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning Juan G Carvajal-Patiño,Vincent Mallet,David Becerra,Luis Fernando Niño Vasquez,Carlos Oliveret al. Nature Communications, 2025, 16 (1), pp.2799. ⟨10.1038/s41467-025-57852-0⟩ Article dans une revue hal-05418823v1
Finding antibodies in cryo-EM maps with CrAI Vincent Mallet,Chiara Rapisarda,Hervé Minoux,Maks Ovsjanikov Bioinformatics, 2025, 41 (5), pp.btaf157. ⟨10.1093/bioinformatics/btaf157⟩ Article dans une revue hal-05418831v1
InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep Fabien Mareuil,Rachel Torchet,Luis Checa Ruano,Vincent Mallet,Michael Nilgeset al. Nucleic Acids Research, 2025, pp.gkaf403. ⟨10.1093/nar/gkaf403⟩ Article dans une revue pasteur-05117181v1
AlignScape, displaying sequence similarity using self-organizing maps Isaac Filella-Merce,Vincent Mallet,Eric Durand,Michaël Nilges,Guillaume Bouvieret al. Frontiers in Bioinformatics, 2024, 4, pp.1321508. ⟨10.3389/fbinf.2024.1321508⟩ Article dans une revue hal-04780460v1
RNAglib: a python package for RNA 2.5 D graphs Vincent Mallet,Carlos Oliver,Jonathan Broadbent,William Hamilton,Jérôme Waldispühl Bioinformatics, 2022, 38 (5), pp.1458-1459. ⟨10.1093/bioinformatics/btab844⟩ Article dans une revue hal-05419508v1
quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories Vincent Mallet,Michael Nilges,Guillaume Bouvier Bioinformatics, 2021, 37 (14), pp.2064-2065. ⟨10.1093/bioinformatics/btaa925⟩ Article dans une revue hal-03122153v1
InDeep: 3D fully convolutional neural networks to assist &lt;i&gt;in silico&lt;/i&gt; drug design on protein–protein interactions Vincent Mallet,Luis Checa Ruano,Alexandra Moine Franel,Michael Nilges,Karen Druartet al. Bioinformatics, 2021, 38 (5), pp.1261 - 1268. ⟨10.1093/bioinformatics/btab849⟩ Article dans une revue pasteur-04102799v1
OptiMol : Optimization of Binding Affinities in Chemical Space for Drug Discovery Jacques Boitreaud,Vincent Mallet,Carlos Oliver,Jérôme Waldispühl Journal of Chemical Information and Modeling, 2020, 60 (12), pp.5658-5666. ⟨10.1021/acs.jcim.0c00833⟩ Article dans une revue hal-03122149v1
Augmented base pairing networks encode RNA-small molecule binding preferences Carlos Oliver,Vincent Mallet,Roman Sarrazin Gendron,Vladimir Reinharz,William l Hamiltonet al. Nucleic Acids Research, 2020, 48 (14), pp.7690-7699. ⟨10.1093/nar/gkaa583⟩ Article dans une revue hal-03122151v1

Communication dans un congrès (1)

ATOMSURF: Surface representation for learning on protein structures Vincent Mallet,Souhaib Attaiki,Yangyang Miao,Bruno E Correia,Maks Ovsjanikov ICLR 2025 - Thirteenth International Conference on Learning Representations, Mar 2025, Singapour, Singapore Communication dans un congrès hal-05418851v1

Pré-publication, Document de travail (2)

Machine Learning for RNA-Targeting Drug Design Wissam Karroucha,Carlos Oliver,Veronique Stoven,Vincent Mallet 2026 Pré-publication, Document de travail hal-05444589v1
Reverse-Complement Equivariant Networks for DNA Sequences Vincent Mallet,Jean-Philippe Vert 2021 Pré-publication, Document de travail hal-03510326v1

Thèse (1)

Geometric deep learning for structural bioinformatics Vincent Mallet Bioinformatics [q-bio.QM]. Université Paris Cité, 2022. English. ⟨NNT : 2022UNIP7006⟩ Thèse tel-03943950v1