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Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…

Computational methods for predicting the interface contacts between proteins come highly sought after for drug discovery as they can significantly advance the accuracy of alternative approaches, such as protein-protein docking, protein…

Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule…

Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph…

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize…

Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid…

While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern…

Predicting the effect of amino acid mutations on enzyme thermodynamic stability (DDG) is fundamental to protein engineering and drug design. While recent deep learning approaches have shown promise, they often process sequence and structure…

Introduction Accurate prediction of protein-protein interactions (PPIs) is crucial for understanding cellular functions and advancing drug development. Existing in-silico methods use direct sequence embeddings from Protein Language Models…

Graph theory and graph mining constitute rich fields of computational techniques to study the structures, topologies and properties of graphs. These techniques constitute a good asset in bioinformatics if there exist efficient methods for…

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based…

Identifying novel functional protein structures is at the heart of molecular engineering and molecular biology, requiring an often computationally exhaustive search. We introduce the use of a Deep Convolutional Generative Adversarial…

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…

Functional connectivity (FC) as derived from fMRI has emerged as a pivotal tool in elucidating the intricacies of various psychiatric disorders and delineating the neural pathways that underpin cognitive and behavioral dynamics inherent to…

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…

Structural information about protein-protein interactions, often missing at the interactome scale, is important for mechanistic understanding of cells and rational discovery of therapeutics. Protein docking provides a computational…

In this study, we tackle the challenging task of predicting secondary structures from protein primary sequences, a pivotal initial stride towards predicting tertiary structures, while yielding crucial insights into protein activity,…