5 papers
RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
Dana Rubin, Allan dos Santos Costa, Manvitha Ponnapati +1
Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable…
Accelerating Protein Molecular Dynamics Simulation with DeepJump
Allan dos Santos Costa, Manvitha Ponnapati, Dana Rubin +2
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) sim…
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery
Peter St. John, Dejun Lin, Polina Binder +89
Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increas…
Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow
Zhonglin Cao, Mario Geiger, Allan dos Santos Costa +6
Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art d…
EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
Allan dos Santos Costa, Ilan Mitnikov, Franco Pellegrini +7
Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of…