Background: DprE1, which is a flavoenzyme, very important for cell wall biosynthesis in Mycobacterium tuberculosis (Mtb) and the pathogenesis, virulence, lethality, stress resistance of host. Drug-resistant challenging global human health issue, necessitating development novel, more effective treatment regimens without adverse effects. DprE1 represents potential therapeutic target. It was explo...

The available drugs against coronavirus disease 2019 (COVOD-19), caused by severe acute respiratory syndrome 2 (SARS-CoV-2), are limited. This study aimed to identify ginger-derived compounds that might neutralize SARS-CoV-2 and prevent its entry into host cells. Ring of ginger were screened spike (S) protein alpha, beta, gamma, delta variants SARS-CoV-2. S FASTA sequence was retrieved from Glo...

Computations with two flavours of dynamical staggered quarks are quite popular at present. There are a number of possible problems with such calculations such as flavour symmetry breaking and non-locality of the square-root of the fourflavour action. In this investigation we shall ignore these and consider only the possible errors introduced through algorithmic approximations. We propose the us...

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling st...

A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics. Protonation states are modeled with different charge sets, and titrating residues sample a Boltzmann distribution of protonation states as the simulation progresses, using Monte Carlo sampling based on GB-derived energies. The method is applied to four different crystal structures o...

Quercetin and daidzin are flavonoid glycoside type compounds that have been found in many plants nutraceuticals. This study aims to examine the vitro cytotoxic selectivity properties of quercetin on breast cervical cancers their molecular interaction stability epidermal growth factor receptor tyrosine kinase (EGFR-TK) by applying docking dynamics (MD) simulations. In anticancer activity was per...

The VHL tumour suppressor gene codes for von-Hippel Lindau (VHL) protein which acts by association with Elongin C and Hypoxia Inducing Factor-1 alpha (HIF). Two functional sub-domains in the protein model of VHL contain binding sites for these proteins. Alpha domain of VHL protein contains the binding site for Elongin C (tumorigenic cluster A) whereas; the beta domain contains the binding site ...

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B...

An accurate prediction of the ligand-receptor binding free energies (ΔG) is a critical step in early stages rational drug design. The Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method popular
 
 approach to estimate ΔG. However, correlations between predicted and experimental ΔG are variable. goal this study investigate various approaches optimize accuracy MM-GBSA met...

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (less than 5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhance...