Implementation of Force Distribution Analysis for Molecular Dynamics simulations

Background: The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA), a method that allows visualizing strain propagation in macromolecules. Results: To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions: Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of ...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Wolfram Stacklies, Christian Seifert, Frauke Graeter
• Keywords: Artificial Intelligence, BMCBI 2011, Internal Strain, Mechanical Stress, Proteins