4 accepted papers
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…
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…