7 accepted papers
A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of synthesizable molecules and suffer from poor coverage. To add…
Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side ch…
Protein interaction modeling is central to protein design, which has been transformed by machine learning with broad applications in drug discovery and beyond. In this landscape, structure-based de novo binder design is most often cast as either conditional generative modeling or sequence optimizati…
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 diffusion or flow-based models for conformer generation require significant computational resources. In this work, we bui…
Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present *Generalist Molecular generative model* (GenMol), a versatile framework that uses only a *single* discrete diffusion model to han…
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop *Proteina*, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a t…
Fragment-based drug discovery, in which molecular fragments are assembled into new molecules with desirable biochemical properties, has achieved great success. However, many fragment-based molecule generation methods show limited exploration beyond the existing fragments in the database as they only…