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Proteins can exhibit dynamic structural flexibility as they carry out their functions, especially in binding regions that interact with other molecules. For the key SARS-CoV-2 spike protein that facilitates COVID-19 infection, studies have…

The widespread availability of large amounts of genomic data on the SARS-CoV-2 virus, as a result of the COVID-19 pandemic, has created an opportunity for researchers to analyze the disease at a level of detail unlike any virus before it.…

The objective of this paper is to provide a mathematical model to construct a barrier that may be useful to prevent the penetration of different viruses (Eg. SARS-COV-2) as well as charged aerosols through the concept of electrostatic…

Structure-based Deep Fusion models were recently shown to outperform several physics- and machine learning-based protein-ligand binding affinity prediction methods. As part of a multi-institutional COVID-19 pandemic response, over 500…

The SARS-CoV-2 spike (S) protein facilitates viral infection, and has been the focus of many structure determination efforts. Its flexible loop regions are known to be involved in protein binding and may adopt multiple conformations. This…

Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…

A recent experimental study found that the binding affinity between the cellular receptor human angiotensin converting enzyme 2 (ACE2) and receptor-binding domain (RBD) in spike (S) protein of novel severe acute respiratory syndrome…

Surges that have been observed at different periods in the number of COVID-19 cases are associated with the emergence of multiple SARS-CoV-2 (Severe Acute Respiratory Virus) variants. The design of methods to support laboratory detection…

Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…

Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solvent-mediated allosteric regulation. The present work describes a multiscale approach…

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies, and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important…

Despite of the fast development of highly effective vaccines to control the current COVID$-$19 pandemic, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the…

Heparin has been found to have antiviral activity against SARS-CoV-2. Here, by means of sliding window docking, molecular dynamics simulations and biochemical assays, we investigate the binding mode of heparin to the virus spike…

The SARS CoV-2 virus emerged at the end of 2019 and rapidly developed several mutated variants, specifically the Delta and Omicron, which demonstrate higher infectivity and escalating infection cases worldwide. The dominant transmission…

The availability of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus data post-COVID has reached exponentially to an enormous magnitude, opening research doors to analyze its behavior. Various studies are conducted by…

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this…

Smokers being witnessed with the mild adverse clinical symptoms of SARS-CoV-2, the in-silico study is intended to explore the effect of nicotine binding to the soluble angiotensin converting enzyme II (ACE2) receptor with or without…

Predicting interactions between biomolecules, such as protein-protein complexes, remains a challenging problem. Despite the many advancements done so far, the performances of docking protocols are deeply dependent on their capability of…

SARS-CoV-2 has characteristics of wide contagion and quick propagation velocity. To analyse the visual information of it, we build a SARS-CoV-2 Microscopic Image Dataset (SC2-MID) with 48 electron microscopic images and also prepare their…

SARS-CoV-2, the causative agent of the disease known as Covid-19, has so far reported around 3,435,000 cases of human infections, including more than 239,000 deaths in 187 countries, with no effective treatment currently available. For this…