ArticleJournal of computational chemistry2015
SDA 7: A modular and parallel implementation of the simulation of diffusional association software.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Evolutionary Pro-To-Thr Mutation in the Intrinsically Disordered Domain of ANP32 Family Members Modulates Their Target Binding Modes.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- What determines sub-diffusive behavior in crowded protein solutions?Biophysical journal · 2024Article
- Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence.Communications biology · 2023Article
- Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence.bioRxiv : the preprint server for biology · 2023Article
- Diffusion of small molecule drugs is affected by surface interactions and crowder proteins.iScience · 2022Article
- Absolute protein quantitation of the mouse macrophage Toll-like receptor and chemotaxis pathways.Scientific data · 2022Article
- GeomBD3: Brownian Dynamics Simulation Software for Biological and Engineered Systems.Journal of chemical information and modeling · 2022Article
- Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing.International journal of molecular sciences · 2022Article
- High affinity protein surface binding through co-engineering of nanoparticles and proteins.Nanoscale · 2022Article
- Investigating Intrinsically Disordered Proteins With Brownian Dynamics.Frontiers in molecular biosciences · 2022Article
- Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study.Frontiers in molecular biosciences · 2022Article
- Molecular Dynamics Simulations of a Catalytic Multivalent Peptide-Nanoparticle Complex.International journal of molecular sciences · 2021Article
- An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase.Communications biology · 2021Article
- Molecular Mechanics Study of Flow and Surface Influence in Ligand-Protein Association.Frontiers in molecular biosciences · 2021Article
- DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions.Nucleic acids research · 2020Article
- NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.Biophysical journal · 2020Article
- Brownian Dynamics Simulations of Biological Molecules.Trends in chemistry · 2019Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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