Journal: Journal of Genetic Engineering & Biotechnology

Article Title: Identification of novel Menin-MLL interaction inhibitors targeting leukemia using in-silico virtual screening and structure-based drug design approaches

doi: 10.1016/j.jgeb.2025.100612

Figure Lengend Snippet: Steered Molecular Dynamics (SMD) analysis of ligand dissociation from the binding pocket of the Menin protein for control and 52,920,501 (a) Pulling distance from the Centre-of-mass (COM) (b) Pulling force applied to the ligand over 500 ps trajectory.

Article Snippet: Steered Molecular Dynamics (SMD) analysis of ligand dissociation from the binding pocket of the Menin protein for control and 52,920,501 (a) Pulling distance from the Centre-of-mass (COM) (b) Pulling force applied to the ligand over 500 ps trajectory.

Techniques: Binding Assay, Control

Journal: The journal of physical chemistry. A

Article Title: Binding Energy Calculations of Anthracene and Rhodamine 6G H-Type Dimers: A Comparative Study of DFT and SMD Methods.

doi: 10.1021/acs.jpca.4c07867

Figure Lengend Snippet: Figure 5. Exemplar SMD plots for the unoptimized geometries: (A) anthracene; (B) R6G. Top plots in blue represent the force change as a function of simulation time, while the bottom plots in red are the displacement as a function of simulation time measured between centers of masses of two monomers. As the dimer is fully dissociated at R = 10 Å, the displacement plots are created to enhance the interactions before that point.

Article Snippet: To address this issue, we present a DFT-based validation of a Steered Molecular Dynamics approach (SMD), which we already successfully applied to anthracene and phenanthrene H-type dimers.20 In this study, we extend it to investigate Rhodamine 6G (R6G) H-type dimers comprehensively by applying a very systematic and progressive approach and covering functionals of increasing complexity.

Techniques: