7 citations · 12 across the 5 of their papers we have counts for
8 papers
From Benchmark to Bench: Can Agents Survive Real-World Drug Discovery?
Pierre Llompart, Levent Guner, Helen Lai +2
Agentic systems increasingly coordinate molecular-design tools, but it is unclear which layer of the stack limits outcomes on real projects. We developed MAGI, an open modular agen…
Ensemble-Conditioned Molecular Design
Ross Irwin, Alessandro Tibo, Jon Paul Janet +1
Molecular design is typically approached as a problem of finding molecules which can adopt a single bioactive conformation. In reality, molecules occupy a distribution over conform…
A decoupled alignment kernel for peptide membrane permeability predictions
Ali Amirahmadi, Gökçe Geylan, Leonardo De Maria +3
Cyclic peptides are promising modalities for targeting intracellular sites; however, cell-membrane permeability remains a key bottleneck, exacerbated by limited public data and the…
FlexiFlow: decomposable flow matching for generation of flexible molecular ensemble
Riccardo Tedoldi, Ola Engkvist, Patrick Bryant +3
Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo desig…
Assay2Mol: large language model-based drug design using BioAssay context
Yifan Deng, Spencer S. Ericksen, Anthony Gitter
Scientific databases aggregate vast amounts of quantitative data alongside descriptive text. In biochemistry, molecule screening assays evaluate candidate molecules' functional res…
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation
Julian Cremer, Ross Irwin, Alessandro Tibo +3
We introduce FLOWR, a novel structure-based framework for the generation and optimization of three-dimensional ligands. FLOWR integrates continuous and categorical flow matching wi…
PepINVENT: Generative peptide design beyond the natural amino acids
Gökçe Geylan, Jon Paul Janet, Alessandro Tibo +7
Peptides play a crucial role in the drug design and discovery whether as a therapeutic modality or a delivery agent. Non-natural amino acids (NNAAs) have been used to enhance the p…
SemlaFlow -- Efficient 3D Molecular Generation with Latent Attention and Equivariant Flow Matching
Ross Irwin, Alessandro Tibo, Jon Paul Janet +1
Methods for jointly generating molecular graphs along with their 3D conformations have gained prominence recently due to their potential impact on structure-based drug design. Curr…