SDA 7: A modular and parallel implementation of the simulation of diffusional association software
Article Swipe
Michael Martinez
,
Neil J. Bruce
,
Julia Romanowska
,
Daria B. Kokh
,
Musa Ozboyaci
,
Xiaofeng Yu
,
Mehmet Ali Öztürk
,
Stefan Richter
,
Rebecca C. Wade
·
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1002/jcc.23971
YOU?
·
· 2015
· Open Access
·
· DOI: https://doi.org/10.1002/jcc.23971
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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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/jcc.23971
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.23971
- OA Status
- hybrid
- Cited By
- 74
- References
- 47
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W1552029653
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https://openalex.org/W1552029653Canonical identifier for this work in OpenAlex
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https://doi.org/10.1002/jcc.23971Digital Object Identifier
- Title
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SDA 7: A modular and parallel implementation of the simulation of diffusional association softwareWork title - Type
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articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2015Year of publication
- Publication date
-
2015-06-29Full publication date if available
- Authors
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Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter, Rebecca C. WadeList of authors in order
- Landing page
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https://doi.org/10.1002/jcc.23971Publisher landing page
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.23971Direct link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jcc.23971Direct OA link when available
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Modular design, Computer science, Software, Association (psychology), Computational science, Parallel computing, Programming language, Psychology, PsychotherapistTop concepts (fields/topics) attached by OpenAlex
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74Total citation count in OpenAlex
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2025: 6, 2024: 5, 2023: 4, 2022: 12, 2021: 9Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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| corresponding_institution_ids | https://openalex.org/I223822909, https://openalex.org/I4210151100, https://openalex.org/I71030271 |
| citation_normalized_percentile.value | 0.92737148 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |