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Experimental evidence suggests that the folding and aggregation of the amyloid $\beta$-protein (A$\beta$) into oligomers is a key pathogenetic event in Alzheimer's disease (AD). Inhibiting the pathologic folding and oligomerization of…

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data,…

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this…

The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…

Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, gene expression, etc. Accurate prediction…

Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands,…

Various theoretical studies have been carried out to infer relevant protein-protein interactions among pathogens and their hosts. Such studies are generally based on preferential attachment of bacteria / virus to their human receptor…

High-throughput preclinical perturbation screens, where the effects of genetic, chemical, or environmental perturbations are systematically tested on disease models, hold significant promise for machine learning-enhanced drug discovery due…

The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…

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…

Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…

Pain is a significant global health issue, and the current treatment options for pain management have limitations in terms of effectiveness, side effects, and potential for addiction. There is a pressing need for improved pain treatments…

Epidemiologic and genetic studies in chronic obstructive pulmonary disease (COPD) and many complex diseases suggest subgroup disparities (e.g., by sex). We consider this problem from the standpoint of integrative analysis where we combine…

Many biologically important ligands of proteins are large, flexible, and often charged molecules that bind to extended regions on the protein surface. It is infeasible or expensive to locate such ligands on proteins with standard methods…

One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a second problem arises, namely the eventual development of…

Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…

We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…

Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…

Designing protein-binding proteins with high affinity is critical in biomedical research and biotechnology. Despite recent advancements targeting specific proteins, the ability to create high-affinity binders for arbitrary protein targets…

Decades after their initial observation in prion-infected brain tissues, the identities of virus-like dense particles, varicose tubules, and oval bodies containing parallel bands and fibrils have remained elusive. Our recent work revealed…