生物大分子
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…
Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a…
We study the post-translational escape of nascent proteins at the ribosomal exit tunnel with the consideration of a real shape atomistic tunnel based on the Protein Data Bank (PDB) structure of the large ribosome subunit of archeon…
Inspired by recent work on anti-covid-19 drugs \cite{2} here we study the Quantitative-structure property relationships(QSPR) of phytochemicals screened against SARS-CoV-2 $3CL^{pro}$ with the help of topological indices like the first…
Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2…
We report the results of our study of approved drugs as potential treatments for COVID 19, based on the application of various bioinformatics predictive methods. The drugs studied include chloroquine, ivermectin, remdesivir, sofosbuvir,…
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…
Liquid-liquid phase separation is the mechanism underlying the formation of biomolecular condensates. Disordered protein regions often drive phase separation, but molecular interactions of disordered protein regions are not well understood,…
Motivation: The coronavirus disease 2019 (COVID-19) caused by a new type of coronavirus has been emerging from China and led to thousands of death globally since December 2019. Despite many groups have engaged in studying the newly emerged…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
RNA-RNA interaction (RRI) is ubiquitous and has complex roles in the cellular functions. In human health studies, miRNA-target and lncRNAs are among an elite class of RRIs that have been extensively studied. Bacterial ncRNA-target and RNA…
The recent appearance of COVID-19 virus has created a global crisis due to unavailability of any vaccine or drug that can effectively and deterministically work against it. Naturally, different possibilities (including herbal medicines…
There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…
Carbohydrates such as the trisaccharide motif LeX are key constituents of cell surfaces. Despite intense research, the interactions between carbohydrates of apposing cells or membranes are not well understood. In this article, we…
Proton nuclear magnetic resonance (1H-NMR) is a widely used tool for chemical structural analysis. However, 1H-NMR spectra suffer from natural aberrations that render computer-assisted automated identification of these spectra difficult,…
To shorten the time required to find effective new drugs, like antivirals, a key parameter to consider is membrane permeability, as a compound intended for an intracellular target with poor permeability will have low efficacy. Here, we…
Virtual screening of phytochemicals was performed through molecular docking, simulation, in silico ADMET and drug-likeness prediction to identify the potential hits that can inhibit the effects of SARS-CoV-2. Considering the published…
Coronaviruses are enveloped, non-segmented positive-sense RNA viruses that have the largest genome among RNA viruses. The genome contains a large replicase ORF encodes nonstructural proteins (NSPs), structural and accessory genes. NSP15 is…
Recent events leading to the worldwide pandemic of COVID-19 have demonstrated the effective use of genomic sequencing technologies to establish the genetic sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the…
Understanding E3 ligase and target substrate interactions are important for cell biology and therapeutic development. However, experimental identification of E3 target relationships is not an easy task due to the labor-intensive nature of…