Vincent Mallet

13
Documents

Publications

Publications

Deposit thumbnail

RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning

Juan G Carvajal-Patiño , Vincent Mallet , David Becerra , Luis Fernando Niño Vasquez , Carlos Oliver et al.

Nature Communications, 2025, 16 (1), pp.2799. ⟨10.1038/s41467-025-57852-0⟩

Article dans une revue hal-05418823v1
Deposit thumbnail

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
Deposit thumbnail

InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep

Fabien Mareuil , Rachel Torchet , Luis Checa Ruano , Vincent Mallet , Michael Nilges et al.

Nucleic Acids Research, 2025, pp.gkaf403. ⟨10.1093/nar/gkaf403⟩

Article dans une revue pasteur-05117181v1
Deposit thumbnail

AlignScape, displaying sequence similarity using self-organizing maps

Isaac Filella-Merce , Vincent Mallet , Eric Durand , Michaël Nilges , Guillaume Bouvier et al.

Frontiers in Bioinformatics, 2024, 4, pp.1321508. ⟨10.3389/fbinf.2024.1321508⟩

Article dans une revue hal-04780460v1
Deposit thumbnail

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
Deposit thumbnail

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
Deposit thumbnail

InDeep: 3D fully convolutional neural networks to assist <i>in silico</i> drug design on protein–protein interactions

Vincent Mallet , Luis Checa Ruano , Alexandra Moine Franel , Michael Nilges , Karen Druart et al.

Bioinformatics, 2021, 38 (5), pp.1261 - 1268. ⟨10.1093/bioinformatics/btab849⟩

Article dans une revue pasteur-04102799v1
Deposit thumbnail

Augmented base pairing networks encode RNA-small molecule binding preferences

Carlos Oliver , Vincent Mallet , Roman Sarrazin Gendron , Vladimir Reinharz , William l Hamilton et al.

Nucleic Acids Research, 2020, 48 (14), pp.7690-7699. ⟨10.1093/nar/gkaa583⟩

Article dans une revue hal-03122151v1

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
Deposit thumbnail

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
Deposit thumbnail

Geometric deep learning for structural bioinformatics

Vincent Mallet

Bioinformatics [q-bio.QM]. Université Paris Cité, 2022. English. ⟨NNT : 2022UNIP7006⟩

Thèse tel-03943950v1