SDA7 – Brownian Dynamics Simulations of Proteins

4. November 2021

Researchers from the Molecular and Cellular Modeling (MCM) group at HITS are developing the software “Simulation of Diffusional Association” (SDA) 7.

SDA7 can be used to carry out Brownian dynamics simulations of the diffusional association in a continuum aqueous solvent of two solute molecules, e.g. proteins, or of a solute molecule to an inorganic surface. SDA7 can also be used to simulate the diffusion of multiple proteins, in dilute or concentrated solutions, e.g., to study the effects of macromolecular crowding.  Recently added features enable modelling of the hydrodynamic and electrostatic interactions in Brownian dynamics simulations of the diffusion of protein molecules in the presence of a surface.

The SDA7 software package is available at https://mcm.h-its.org/sda7 and part of the functionality is implemented in the webserver version, webSDA.

References:

Reinhardt M, Bruce NJ, Kokh DB, Wade RC (2021). Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics, J. Chem. Theory Comput. 17(6):3510-3524

Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC (2015). SDA 7: A modular and parallel implementation of the simulation of diffusional association software, J. Comput. Chem. 36(21):1631-1645

Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC (2015). webSDA: a web server to simulate macromolecular diffusional association, Nucleic Acids Res 43(W1):W220-W224

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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