FDA – detect and follow force in proteins
Force distribution analysis (FDA) is a method to detect and follow force and stress propagation in proteins, reminiscent of Finite Element Analysis used to engineer macroscopic structures. The method is based on Molecular Dynamics (MD) simulations during which we directly calculate forces between each atom pair in a system. The most recent version of FDA is now implemented in the MD simulation package GROMACS-2020 (https://manual.gromacs.org/documentation/2020/index.html). Recent applications of FDA include the stress concentration in collagen and the allosteric effect of disulfide bonding in von Willebrand factor.
Watch the video about a graphene sheet broken by an AFM (atomic force microscope) tip here.
The FDA code was developed by the Molecular Biomechanics (MBM) group at HITS can be downloaded on GitHub: https://github.com/HITS-MBM/gromacs-fda
References:
Paper: Costescu BI, Gräter F. Time-resolved force distribution analysis. BMC Biophys. 2013;6:5. doi: 10.1186/2046-1682-6-5: https://bmcbiophys.biomedcentral.com/articles/10.1186/2046-1682-6-5
Example: https://www.h-its.org/projects/force-triggered-blood-coagulation/
About HITS
HITS, the Heidelberg Institute for Theoretical Studies, was established in 2010 by physicist and SAP co-founder Klaus Tschira (1940-2015) and the Klaus Tschira Foundation as a private, non-profit research institute. HITS conducts basic research in the natural, mathematical, and computer sciences. Major research directions include complex simulations across scales, making sense of data, and enabling science via computational research. Application areas range from molecular biology to astrophysics. An essential characteristic of the Institute is interdisciplinarity, implemented in numerous cross-group and cross-disciplinary projects. The base funding of HITS is provided by the Klaus Tschira Foundation.
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