6 accepted papers
Machine learning methods that predict protein fitness from sequence remain sensitive to changes in data distributions, limiting generalization across common conditions encountered in protein engineering. Practically, protein engineers are thus left wondering about the effective utility of ML tools. …
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…
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…
Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Although the 3D molecular graph structure is necessary for models to achieve strong performance on many tasks, it is infeasible to obtain 3D structures at the scale required by…
Machine learning could enable an unprecedented level of control in protein engineering for therapeutic and industrial applications. Critical to its use in designing proteins with desired properties, machine learning models must capture the protein sequence-function relationship, often termed fitness…