ArticleFrontiers in molecular biosciences2019
DFMD: Fast and Effective DelPhiForce Steered Molecular Dynamics Approach to Model Ligand Approach Toward a Receptor: Application to Spermine Synthase Enzyme.
Article in Frontiers in molecular biosciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.Journal of computational chemistry · 2025Article
- Secondary Binding Site of CYP17A1 in Enhanced Sampling Simulations.Journal of chemical information and modeling · 2024Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.Journal of chemical theory and computation · 2022Article
- Long-range electrostatic interactions significantly modulate the affinity of dynein for microtubules.Biophysical journal · 2022Article
- StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions.Frontiers in molecular biosciences · 2020Article
- Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2.Frontiers in molecular biosciences · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Here we report a novel approach, the DelPhiForce Molecular Dynamics (DFMD) method, for steered molecular dynamics simulations to model receptor-ligand association involving charged species. The main purpose of developing DFMD is to simulate ligand's trajectory toward the receptor and thus to predict the "entrance" of the binding pocket and conformational changes associated with the binding. We demonstrate that the DFMD is superior compared with molecular dynamics simulations applying standard cut-offs, provides correct binding forces, allows for modeling the ligand approach at long distances and thus guides the ligand toward the correct binding spot, and it is very fast (frequently the binding is completed in <1 ns). The DFMD is applied to model the binding of two ligands to a receptor (spermine synthase) and it is demonstrated that it guides the ligands toward the corresponding pockets despite of the initial ligand's position with respect to the receptor. Predicted conformational changes and the order of ligand binding are experimentally verified.
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