Evaluation of protein–ligand affinity prediction using steered molecular dynamics simulations

2016 ◽  
Vol 35 (15) ◽  
pp. 3221-3231 ◽  
Author(s):  
Noriaki Okimoto ◽  
Atsushi Suenaga ◽  
Makoto Taiji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Steered Molecular Dynamics ◽  
Affinity Prediction ◽  
Ligand Affinity ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

2013 ◽  
Vol 4 ◽  
pp. 429-440 ◽  
Author(s):  
Hlengisizwe Ndlovu ◽  
Alison E Ashcroft ◽  
Sheena E Radford ◽  
Sarah A Harris
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Steered Molecular Dynamics ◽  
Mechanical Failure ◽  
Structural Defects ◽  
Dynamics Simulations

We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

The talin–integrin interface under mechanical stress

2014 ◽  
Vol 10 (12) ◽  
pp. 3217-3228 ◽  
Author(s):  
Sampo Kukkurainen ◽  
Juha A. Määttä ◽  
John Saeger ◽  
Jarkko Valjakka ◽  
Viola Vogel ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Mechanical Stress ◽  
Steered Molecular Dynamics ◽  
Dynamics Simulations

Interactions and force resistance of different β-integrin–talin complexes were analysed in a set of steered molecular dynamics simulations.

scholarly journals Steered molecular dynamics simulations reveal the role of Ca2+ in regulating mechanostability of cellulose-binding proteins

2018 ◽  
Vol 20 (35) ◽  
pp. 22674-22680 ◽  
Author(s):  
Melissabye Gunnoo ◽  
Pierre-André Cazade ◽  
Adam Orlowski ◽  
Mateusz Chwastyk ◽  
Haipei Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Proteins ◽  
Mechanical Stability ◽  
Binding Specificity ◽  
Steered Molecular Dynamics ◽  
Dynamics Simulations ◽  
Cellulose Binding ◽  
High Mechanical Stability

Cellulosome nanomachines utilise binding specificity and high mechanical stability in breaking down cellulose.

How strong are hydrogen bonds in the peptide model?

2020 ◽  
Vol 22 (3) ◽  
pp. 1392-1399
Author(s):  
Jakub Dąbrowski ◽  
Wiesław Nowak ◽  
Arkadiusz Ptak
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Molecular Dynamics Simulations ◽  
Force Spectroscopy ◽  
Steered Molecular Dynamics ◽  
Dynamic Force ◽  
Dynamic Force Spectroscopy ◽  
Dynamics Simulations

We provide a methodology based on the steered molecular dynamics simulations and dynamic force spectroscopy calculations to determine the kinetic and energetic characteristics of hydrogen bonds.

Sign in / Sign up

Export Citation Format

Share Document