The study of in silico molecular docking analysis of such derivatives to determine the binding affinity, residual interaction, and hydrogen bonding of several 2H-thiopyrano[2,3-b]quinolines against CB1a is reported here. The current work demonstrated that 2H-thiopyrano[2,3...
Molecular dockingscoring functionsrandom forestchemical informaticsstructural bioinformaticsDocking is a structure-based computational tool that can be used to predict the strength with which a small ligand molecule binds to a macromolecular target. Such binding affinity prediction is crucial to design ...
In this study we have explored other naphthofuran derivatives for their potential to inhibit BACE-1 and GSK-3 through docking, molecular dynamics, binding energy (MM-PBSA). These computational methods were performed to estimate the binding affinity of naphthofuran derivatives towards the BACE-1 and...
most molecular or drug design strategies are centered around the optimization of the binding affinity; however, the behavior and the response of a ligand to changes in the environment or in the protein target are different for enthalpic or entropic molecules, even if the binding affinity is the ...
A larger binding energy for primary binding also indicated that paclitaxel showed higher binding affinity mainly due to the stronger hydrogen bonding interactions. There was a significant difference between the two complexes on structure according to the dssp results. Moreover, structure of the binding...
Its transition makes a major change in the protein and its binding affinity. The ligand binding aggrecanases can be influenced by Zn2+ ions; therefore the study focuses on checking the binding mode in the presence and absence of zinc using Docking and Molecular dynamics simulation. The crystal ...
We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit d...
Human serum albumin (HSA)-drug binding affinity is one of the major factors that determine the pharmacokinetics, halftime and bioavailability of drugs in v... Mohsen,Shahlaei,Behnoosh,... - 《Journal of Luminescence》 被引量: 18发表: 2015年 Spectroscopic, docking and molecular dynamics simulatio...
In this work, we develop an FMO-based binding affinity calculation method (FMOScore) with linear fitting on terms including solvation free energy, calculated by the PM7/COSMO model [50], and the deformation energy term of ligands. When the entropy term, calculated with the interaction entropy...
compounds IMP (inhibitor with known binding parameters [17]) and GMP. We focused on free compounds because in our previous work we did not observe significant difference in hydrolysis when compounds (m7GpppG or GpppG) were bound to the RNA chain [12]. To study the binding affinity, we ...