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In this paper, a new method for PPI (proteinprotein interaction) prediction is proposed. In PPI prediction, a reliable and sufficient number of training samples is not available, but a large number of unlabeled samples is in hand. In the…

Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional…

Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale…

Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods…

Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems, and aligning multiple PPI networks can reveal important functional relationships between different species. However, assessing the…

Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…

Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…

Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…

Protein-protein interactions (PPIs) are critical for various biological processes, and understanding their dynamics is essential for decoding molecular mechanisms and advancing fields such as cancer research and drug discovery. Mutations in…

Motivation: Protein-protein interactions (PPIs) are usually modelled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They…

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…

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…

Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences…

The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…

Protein Structure Prediction (PSP) is an unsolved problem in the field of computational biology. The problem of protein structure prediction is about predicting the native conformation of a protein, while its sequence of amino acids is…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…

Decoding protein-protein interactions (PPIs) at the residue level is crucial for understanding cellular mechanisms and developing targeted therapeutics. We present Seq2Bind Webserver, a computational framework that leverages fine-tuned…

We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…

Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs)…