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Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…

Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability…

Identifying protein-protein interactions (PPI) is crucial for gaining in-depth insights into numerous biological processes within cells and holds significant guiding value in areas such as drug development and disease treatment. Currently,…

Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design. The high-throughput experiments…

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…

Computational protein-protein interaction (PPI) prediction techniques can contribute greatly in reducing time, cost and false-positive interactions compared to experimental approaches. Sequence is one of the key and primary information of…

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…

Protein-protein interactions (PPIs) are fundamental for deciphering cellular functions,disease pathways,and drug discovery.Although existing neural networks and machine learning methods have achieved high accuracy in PPI prediction,their…

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…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

Protein-protein interaction (PPI) prediction is an instrumental means in elucidating the mechanisms underlying cellular operations, holding significant practical implications for the realms of pharmaceutical development and clinical…

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…

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but often lack the structural knowledge essential for some biological applications. To address this, we introduce a method to…

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…

Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find…

The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…

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…

Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…