Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating proteins with only static target properties, such as motifs and symmetries. In this work, we take a step towards overcoming this limitation by proposing a framework to condition structure generation on flexibility, which is crucial for key functionalities such as catalysis or molecular recognition. We first introduce BackFlip, an equivariant neural network for predicting per-residue flexibility from an input backbone structure. Relying on BackFlip, we propose FliPS, an SE(3)-equivariant conditional flow matching model that solves the inverse problem, that is, generating backbones that display a target flexibility profile. In our experiments, we show that FliPS is able to generate novel and diverse protein backbones with the desired flexibility, verified by Molecular Dynamics (MD) simulations. FliPS and BackFlip are available at https://github.com/graeter-group/flips.

Deep generative models have recently been proposed for sampling protein conformations from the Boltzmann distribution, as an alternative to often prohibitively expensive Molecular Dynamics simulations. However, current state-of-the-art approaches rely on fine-tuning pre-trained folding models and evolutionary sequence information, limiting their applicability and efficiency, and introducing potential biases. In this work, we propose a flow matching model for sampling protein conformations based solely on backbone geometry - BBFlow. We introduce a geometric encoding of the backbone equilibrium structure as input and propose to condition not only the flow but also the prior distribution on the respective equilibrium structure, eliminating the need for evolutionary information. The resulting model is orders of magnitudes faster than current state-of-the-art approaches at comparable accuracy, is transferable to multi-chain proteins, and can be trained from scratch in a few GPU days. In our experiments, we demonstrate that the proposed model achieves competitive performance with reduced inference time, across not only an established benchmark of naturally occurring proteins but also de novo proteins, for which evolutionary information is scarce or absent. BBFlow is available at https://github.com/graeter-group/bbflow.

In practice, domain shifts are likely to occur between training and test data, necessitating domain adaptation (DA) to adjust the pre-trained source model to the target domain. Recently, universal domain adaptation (UniDA) has gained attention for addressing the possibility of an additional category (label) shift between the source and target domain. This means new classes can appear in the target data, some source classes may no longer be present, or both at the same time. For practical applicability, UniDA methods must handle both source-free and online scenarios, enabling adaptation without access to the source data and performing batch-wise updates in parallel with prediction. In an online setting, preserving knowledge across batches is crucial. However, existing methods often require substantial memory, which is impractical because memory is limited and valuable, in particular on embedded systems. Therefore, we consider memory-efficiency as an additional constraint. To achieve memory-efficient online source-free universal domain adaptation (SF-UniDA), we propose a novel method that continuously captures the distribution of known classes in the feature space using a Gaussian mixture model (GMM). This approach, combined with entropy-based out-of-distribution detection, allows for the generation of reliable pseudo-labels. Finally, we combine a contrastive loss with a KL divergence loss to perform the adaptation. Our approach not only achieves state-of-the-art results in all experiments on the DomainNet and Office-Home datasets but also significantly outperforms the existing methods on the challenging VisDA-C dataset, setting a new benchmark for online SF-UniDA. Our code is available at https://github.com/pascalschlachter/GMM.

We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA) architecture from AlphaFold2, in which the backbone residue frames and geometric features are represented in the projective geometric algebra. This enables to construct geometrically expressive messages between residues, including higher order terms, using the bilinear operations of the algebra. We evaluate our architecture by incorporating it into the framework of FrameFlow, a state-of-the-art flow matching model for protein backbone generation. The proposed model achieves high designability, diversity and novelty, while also sampling protein backbones that follow the statistical distribution of secondary structure elements found in naturally occurring proteins, a property so far only insufficiently achieved by many state-of-the-art generative models.