The conventional view of a protein structure as static provides only a limited picture. There is increasing evidence that protein dynamics are often vital to protein function including interaction with partners such as other proteins, nucleic acids, and small molecules. Considering flexibility is also important in applications such as computational protein docking and protein design. While resi...

It is crucial to consider dynamics for understanding the biological function of proteins. We used a large number of molecular dynamics (MD) trajectories of nonhomologous proteins as references and examined static structural features of proteins that are most relevant to fluctuations. We examined correlation of individual structural features with fluctuations and further investigated effective c...

The bacterial Obg proteins (Spo0B-associated GTP-binding protein) belong to the subfamily of P-loop GTPase proteins that contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain which is referred as the "Obg fold" and now it is considered as one of the new targets for antibacterial drug. When the Obg protein is associated with GTP, ...

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to h...

Multifunctional enzyme engineering can improve enzyme cocktails for emerging biofuel technology. Molecular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental validation. This study describes the computational design of a bifunctional xylanase...

By a molecular dynamics (MD) simulation method which ensures the system will be under hydrostatic pressure, dynamic and elastic properties of glassy metatstable states are investigated. In MD method, cell fluctuates not only in volume but also shape constant pressure temperature. As observed experiments for many glass forming materials, metastable our show sharp increase mean-square-displacemen...

Outbreak of coronavirus seems to have exacerbated across the globe, but drugs not been discovered till now. Due having antiviral activity D-glucopyranoside derivatives, this study was designed examine as inhibitor by in sillico against main protease (Mpro) and Spike (Spro) SARS-CoV-2. First, these derivatives were optimised Density Functional Theory (DFT). The observation monitored molecular do...

Protein motions play important roles in numerous biological processes such as enzyme catalysis, muscle contractions, antigen-antibody interactions, gene regulation and virus assembly. Knowledge of protein flexibility is also important in rational drug design, protein docking and protein engineering. However, the experimental measurement of protein motions is often difficult, requiring sophistic...

In this research, the fourteen commonly used antiviral drugs were investigated through computational tools against CoV-19 or SARS-2, as well two small bioactive molecules from cannabis plant, Tetrahydrocannabinol (THC) and Cannabinol (CBN). Thus, these selelcted for molecular docking main protein (5r7y) spike (6xs6) of coronavirus. It was illustrated that binding energies Mpro Pimodivir, Baloxa...

Simple expressions allowing estimation of the turbulent density perturbation from the reflectometry phase root mean square (r.m.s.) measurements and accounting for the turbulence correlation length are given. The numerical procedure for precise turbulence radial profile reconstruction for different turbulence wave number spectra and both O-mode and X-mode reflectometry is proposed. It is valida...