Screening of Potential Inhibitors Targeting the Main Protease Structure of SARS-CoV-2 via Molecular Docking, and Approach with Molecular Dynamics, RMSD, RMSF, H-Bond, SASA and MMGBSA

Bioinformatic investigation of Nipah virus surface protein mutations: Molecular docking with Ephrin B2 receptor, molecular dynamics simulation, and structural impact analysis

“…This observation underscores the relative similarity in the structural dynamics or flexibility of the systems under scrutiny. 59,60 The marginal variations in the RMSF values between these conditions may indicate a certain degree of structural stability or shared conformational behavior within the studied systems. It is important to note that while the differences in RMSF may not be pronounced, they may still hold functional or biophysical relevance.…”

“…This information is used to understand how mobile or stable are different regions of the protein. [59][60][61] Therefore, it is essential to understand RMSF. The Figure 5 results collectively suggest that the introduction of the G273S mutation leads to a moderately increased structural deviation (as indicated by RMSD) and flexibility (as indicated by RMSF) in the Nipah virus F protein.…”

“…Furthermore, it is noteworthy that neither mutation induces substantial alterations in the protein structure, as evidenced by the relatively small RMSD and RMSF variations. [59][60][61][62] The wild-type F protein displays a stable structural profile, although it does exhibit a comparable degree of flexibility to the D252G mutant. 59,61 These findings collectively imply that while the mutations G273S and D252G do influence the structural dynamics of the Nipah virus F protein, the observed differences, although statistically significant, are relatively subtle.…”

“…[59][60][61][62] The wild-type F protein displays a stable structural profile, although it does exhibit a comparable degree of flexibility to the D252G mutant. 59,61 These findings collectively imply that while the mutations G273S and D252G do influence the structural dynamics of the Nipah virus F protein, the observed differences, although statistically significant, are relatively subtle. Understanding the effects of mutations is vital in vaccine development, as certain mutations can compromise the efficacy of vaccines by altering the virus's antigenic properties or hindering the effectiveness of antiviral drugs.…”

Design, synthesis, biological evaluation and molecular docking studies of quinoline-anthranilic acid hybrids as potent anti-inflammatory drugs

“…It quantifies Organic & Biomolecular Chemistry Paper the structural deviation between the initial and final conformations of a biomolecular system, thus providing insights into the stability and accuracy of the simulation. 49 RMSD is calculated by measuring the average displacement of atoms in a simulated structure relative to a reference structure over time which offers an assessment of the convergence and reliability of MD simulations, ensuring that the modeled molecular dynamics accurately reflect the real behavior of biomolecules. 50 The plots in Fig.…”