title: SDA 7: A modular and parallel implementation of the simulation of diffusional association software.
abstract: The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein-protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration-dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object-oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance.
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Martinez
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Bruce
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Romanowska
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Daria B
authors.initials: DB
authors.lastname: Kokh
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.|Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp), Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
authors.forename: Musa
authors.initials: M
authors.lastname: Ozboyaci
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.|Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Im Neuenheimer Feld 501, 69120, Heidelberg, Germany.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Yu
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.|Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Im Neuenheimer Feld 501, 69120, Heidelberg, Germany.
authors.forename: Mehmet Ali
authors.initials: MA
authors.lastname: Öztürk
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Richter
authors.affiliation: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.|Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.|Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Wade
mesh_terms: D000465:Algorithms; D001407:Bacillus / Q000201:enzymology; D001426:Bacterial Proteins; D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry; D012260:Ribonucleases / Q000737:chemistry; D012984:Software
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease
keywords: Brownian dynamics; biomacromolecular diffusion; macromolecular association; parallelization; protein adsorption; protein flexibility; protein-solid state interactions