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Background. Human aging is linked to many prevalent diseases. The aging process is highly influenced by genetic factors. Hence, it is important to identify human aging-related genes. We focus on supervised prediction of such genes. Gene…
Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein…
Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…
PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…
Graphical user interface (GUI) has become integral to modern society, making it crucial to be understood for human-centric systems. However, unlike natural images or documents, GUIs comprise artificially designed graphical elements arranged…
In the field of materials science, comprehending material properties is often hindered by the complexity of datasets originating from various sources. This study introduces the Automated Model Training (AMT) Graphical User Interface (GUI),…
A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often…
In silico prediction of drug-target interactions (DTI) is significant for drug discovery because it can largely reduce timelines and costs in the drug development process. Specifically, deep learning-based DTI approaches have been shown…
Knowledge graphs (KGs) provide reliable external knowledge for a wide variety of AI tasks in the form of structured triples. Knowledge graph pre-training (KGP) aims to pre-train neural networks on large-scale KGs and provide unified…
Graphical User Interface (GUI) agents, powered by Large Foundation Models, have emerged as a transformative approach to automating human-computer interaction. These agents autonomously interact with digital systems or software applications…
Protein Contact Network (PCN) is a powerful tool for analysing the structure and function of proteins. In particular, PCN has been used for disclosing the molecular features of allosteric regulation through PCN clustering. Such analysis is…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
We introduce a new, simplified model of proteins, which we call protein metastructure. The metastructure of a protein carries information about its secondary structure and $\beta$-strand conformations. Furthermore, protein metastructure…
The recent rise of cryo-EM and X-ray high-throughput techniques is providing a wealth of new structures trapped in different conformations. Understanding how proteins transition between different conformers, and how they relate to each…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The integration of bioinformatics predictions and experimental validation plays a pivotal role in advancing biological research, from understanding molecular mechanisms to developing therapeutic strategies. Bioinformatics tools and methods…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various…
SkeleDock is a scaffold docking algorithm which uses the structure of a protein-ligand complex as a template to model the binding mode of a chemically similar system. This algorithm was evaluated in the D3R Grand Challenge 4 pose prediction…