生物大分子
Naloxone, an opioid antagonist, has been widely used to save lives from opioid overdose, a leading cause for death in the opioid epidemic. However, naloxone has short brain retention ability, which limits its therapeutic efficacy.…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
Here after performing docking and molecular dynamics of various small molecules derived as a secondary metabolite from fungi, we propose Flaviolin to act as potent inhibitor of 3-chymotrypsin (3C) like protease (3CLpro) of noval corona…
The world has witnessed unprecedented human and economic loss from the COVID-19 disease, caused by the novel coronavirus SARS-CoV-2. Extensive research is being conducted across the globe to identify therapeutic agents against the…
Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the…
SARS-COV-2 identified as COVID-19 in Wuhan city of China in the month of December, 2019 has now been declared as pandemic by World Health Organization whose transmission chain and cure both have emerged as a tough problem for the medical…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…
Thermodynamic profiles, based on bioinformatic hydropathicity scales and membrane-fitted sliding windows, exhibit accurately level sets of hydrophobic peaks or valleys in the constant fragment Fc of monoclonal antibodies. These sets provide…
Identifying protein-protein interactions is crucial for a systems-level understanding of the cell. Recently, algorithms based on inverse statistical physics, e.g. Direct Coupling Analysis (DCA), have allowed to use evolutionarily related…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Determining which proteins interact together is crucial to a systems-level understanding of the cell. Recently, algorithms based on Direct Coupling Analysis (DCA) pairwise maximum-entropy models have allowed to identify interaction partners…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
The fast and untraceable virus mutations take lives of thousands of people before the immune system can produce the inhibitory antibody. Recent outbreak of novel coronavirus infected and killed thousands of people in the world. Rapid…
Here we propose that the upper bound marginal stability of proteins (7.4 kcal/mol) is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and Post-Translational…
Biosyntheses of proteins, nucleotides and fatty acids, are essential for the malignant proliferation and survival of cancer cells. Cumulating research findings show that amino acid restrictions are potential strategies for cancer…
Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use of hydrogen bonds which are important for secondary…
Coronaviruses are a class of virus responsible of the recent outbreak of Human Severe Acute Respiratory Syndrome. The molecular machinery behind the viral entry and thus infectivity is based on the formation of the complex of virus spike…
A library of substituted pyrimidines was synthesized and evaluated for free radical scavenging, and in vitro cytotoxic activity in 3T3 cells. All compounds showed good free radical scavenging activity with IC50 values in the range of 42.9 +…
Coronavirus (COVID-19) outbreak in late 2019 and 2020 comprises a serious and more likely a pandemic threat worldwide. Given that the disease has not approved vaccines or drugs up to now, any efforts for drug design and or clinical trails…