FDA – detect and follow force in proteins

5. July 2021

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

The Heidelberg Institute for Theoretical Studies (HITS) was established in 2010 by the 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 sciences, mathematics and computer science, with a focus on the processing, structuring, and analyzing of large amounts of complex data and the development of computational methods and software. The research fields range from molecular biology to astrophysics. The shareholders of HITS are the HITS-Stiftung, which is a subsidiary of the Klaus Tschira Foundation, Heidelberg University and the Karlsruhe Institute of Technology (KIT). HITS also cooperates with other universities and research institutes and with industrial partners. The base funding of HITS is provided by the HITS Stiftung with funds received from the Klaus Tschira Foundation. The primary external funding agencies are the Federal Ministry of Education and Research (BMBF), the German Research Foundation (DFG), and the European Union.

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