Related papers: ViraHinter: a dual-modal artificial intelligence f…
We demonstrate that Protein-Protein Interaction (PPI) networks in several eucaryotic organisms contain significantly more self-interacting proteins than expected if such homodimers randomly appeared in the course of the evolution. We also…
The development of therapeutic targets for COVID-19 treatment is based on the understanding of the molecular mechanism of pathogenesis. The identification of genes and proteins involved in the infection mechanism is the key to shed out…
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…
The Influenza virus can be considered as one of the most severe viruses that can infect multiple species with often fatal consequences to the hosts. The Hemagglutinin (HA) gene of the virus can be a target for antiviral drug development…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
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…
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interacting patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number…
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an…
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…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…
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…
Recent technological advances have introduced new high-throughput methods for studying host-virus interactions, but testing synergistic interactions between host gene pairs during infection remains relatively slow and labor intensive.…
Physical Human-Humanoid Interaction (pHHI) is a rapidly advancing field with significant implications for deploying robots in unstructured, human-centric environments. In this review, we examine the current state of the art in pHHI through…
Mitochondrial diseases are largely caused by dysfunction in mitochondrial proteins. However, annotations of human mitochondrial proteins are scattered across various public databases and individual studies. To facilitate research aimed at…
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,…
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…
Motivation: Discovering functional modules in protein-protein interaction (PPI) networks by optimization methods remains a longstanding challenge in biology. Traditional algorithms simply consider strong protein complexes that can be found…
Protein-protein interactions are central mediators in many biological processes. Accurately predicting the effects of mutations on interactions is crucial for guiding the modulation of these interactions, thereby playing a significant role…
Knowledge about protein-protein interactions is essential in understanding the biological processes such as metabolic pathways, DNA replication, and transcription etc. However, a majority of the existing Protein-Protein Interaction (PPI)…