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Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been…
Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence…
While most studies emphasize on certain aspects of Pathogen-Host Interactions (PHI), such as the preferential attachment of bacteria or virus to its human receptor homolog, studies have attempted to methodically classify interactions among…
The identification of essential proteins in protein-protein interaction networks (PINs) can help to discover drug targets and prevent disease. In order to improve the accuracy of the identification of essential proteins, researchers…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Traditional drug discovery processes are both time-consuming and require extensive professional expertise. With the accumulation of drug-target interaction (DTI) data from experimental studies, leveraging modern machine-learning techniques…
We instruct an AI agent to construct two separate agentic AI platforms: one for autonomous training of predictive ML models for human-human and virus-human PPI, and the other for inducing explicit general rules governing human-human and…
The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a query…
The ongoing opioid crisis highlights the urgent need for novel therapeutic strategies that can be rapidly deployed. This study presents a novel approach to identify potential repurposable drugs for the treatment of opioid addiction, aiming…
Biomedical research has revealed the crucial role of miRNAs in the progression of many diseases, and computational prediction methods are increasingly proposed for assisting biological experiments to verify miRNA-disease associations…
Identifying the entire set of complexes is essential not only to understand complex formations, but also to map the high level organisation of the cell. Computational prediction of protein complexes faces several challenges including the…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the…
Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance…
Opioid use disorder (OUD) continuously poses major public health challenges and social implications worldwide with dramatic rise of opioid dependence leading to potential abuse. Despite that a few pharmacological agents have been approved…
Owing to the complexity of higher eukaryotic cells, a complete proteome is likely to be very difficult to achieve. However, advantage can be taken of the cell compartmentalization to build organelle proteomes, which can moreover be viewed…
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…