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webSDA: a web server to simulate macromolecular diffusional association.

Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC - Nucleic Acids Res. (2015)

Bottom Line: Macromolecular interactions play a crucial role in biological systems.Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: 'SDA docking' to generate structures of the diffusional encounter complexes of two macromolecules, 'SDA association' to calculate bimolecular diffusional association rate constants, and 'SDA multiple molecules' to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-W├╝rttemberg, Germany Rebecca.Wade@h-its.org.

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Related in: MedlinePlus

Workflow of webSDA.
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Related In: Results  -  Collection

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Figure 1: Workflow of webSDA.

Mentions: The workflow of webSDA is shown in Figure 1.


webSDA: a web server to simulate macromolecular diffusional association.

Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC - Nucleic Acids Res. (2015)

Workflow of webSDA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489311&req=5

Figure 1: Workflow of webSDA.
Mentions: The workflow of webSDA is shown in Figure 1.

Bottom Line: Macromolecular interactions play a crucial role in biological systems.Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: 'SDA docking' to generate structures of the diffusional encounter complexes of two macromolecules, 'SDA association' to calculate bimolecular diffusional association rate constants, and 'SDA multiple molecules' to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-W├╝rttemberg, Germany Rebecca.Wade@h-its.org.

Show MeSH
Related in: MedlinePlus