tetano
Editor, Senior Moderator
J Mol Graph Model. 2017 Aug 24;77:137-142. doi: 10.1016/j.jmgm.2017.08.018. [Epub ahead of print]
[h=1]Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations.[/h] Tam NM[SUP]1[/SUP], Nguyen MT[SUP]2[/SUP], Ngo ST[SUP]3[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0.82 and error of σΔG[SUB]exp[/SUB]=2.2kcal/mol. The results were observed using Amber99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy.
Copyright ? 2017 Elsevier Inc. All rights reserved.
[h=4]KEYWORDS:[/h] Absolute affinity; Fast pulling of ligand; Interaction energy; NEMD; Neuraminidase; Pulling work
PMID: 28854402 DOI: 10.1016/j.jmgm.2017.08.018
[h=1]Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations.[/h] Tam NM[SUP]1[/SUP], Nguyen MT[SUP]2[/SUP], Ngo ST[SUP]3[/SUP].
[h=3]Author information[/h]
[h=3]Abstract[/h] The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der Waals (vdW) interactions. The finding indicates that vdW metric is dominant over electrostatics in binding process. The computed values are in good agreement with experimental data with a correlation coefficient of R=0.82 and error of σΔG[SUB]exp[/SUB]=2.2kcal/mol. The results were observed using Amber99SB-ILDN force field in comparison with CHARMM27 and GROMOS96 43a1 force fields. Obtained results may stimulate the search for an Influenza therapy.
Copyright ? 2017 Elsevier Inc. All rights reserved.
[h=4]KEYWORDS:[/h] Absolute affinity; Fast pulling of ligand; Interaction energy; NEMD; Neuraminidase; Pulling work
PMID: 28854402 DOI: 10.1016/j.jmgm.2017.08.018