Next Article in Journal
Cytotoxicity of Triterpenes from Green Walnut Husks of Juglans mandshurica Maxim in HepG-2 Cancer Cells
Previous Article in Journal
γ-Alumina Nanoparticle Catalyzed Efficient Synthesis of Highly Substituted Imidazoles
Article Menu

Export Article

Open AccessArticle
Molecules 2015, 20(10), 19236-19251; doi:10.3390/molecules201019236

A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes

1
State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China
2
School of Mechanical Engineering, Dalian University of Technology, Dalian 116023, China
*
Author to whom correspondence should be addressed.
Academic Editor: James Gauld
Received: 31 August 2015 / Revised: 14 October 2015 / Accepted: 14 October 2015 / Published: 22 October 2015
(This article belongs to the Section Medicinal Chemistry)
View Full-Text   |   Download PDF [1790 KB, uploaded 22 October 2015]   |  

Abstract

Binding affinity prediction of protein–ligand complexes has attracted widespread interest. In this study, a self-adaptive steered molecular dynamics (SMD) method is proposed to reveal the binding affinity of protein–ligand complexes. The SMD method is executed through adjusting pulling direction to find an optimum trajectory of ligand dissociation, which is realized by minimizing the stretching force automatically. The SMD method is then used to simulate the dissociations of 19 common protein–ligand complexes which are derived from two homology families, and the binding free energy values are gained through experimental techniques. Results show that the proposed SMD method follows a different dissociation pathway with lower a rupture force and energy barrier when compared with the conventional SMD method, and further analysis indicates the rupture forces of the complexes in the same protein family correlate well with their binding free energy, which reveals the possibility of using the proposed SMD method to identify the active ligand. View Full-Text
Keywords: binding affinity; steered molecular dynamics; rupture force; protein–ligand unbinding; optimization binding affinity; steered molecular dynamics; rupture force; protein–ligand unbinding; optimization
Figures

Figure 1a

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Gu, J.; Li, H.; Wang, X. A Self-Adaptive Steered Molecular Dynamics Method Based on Minimization of Stretching Force Reveals the Binding Affinity of Protein–Ligand Complexes. Molecules 2015, 20, 19236-19251.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]

Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top