webSDA: a web server to simulate macromolecular diffusional association

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 Brownia...

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Autores principales: Yu, Xiaofeng, Martinez, Michael, Gable, Annika L., Fuller, Jonathan C., Bruce, Neil J., Richter, Stefan, Wade, Rebecca C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489311/
https://www.ncbi.nlm.nih.gov/pubmed/25883142
http://dx.doi.org/10.1093/nar/gkv335
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author Yu, Xiaofeng
Martinez, Michael
Gable, Annika L.
Fuller, Jonathan C.
Bruce, Neil J.
Richter, Stefan
Wade, Rebecca C.
author_facet Yu, Xiaofeng
Martinez, Michael
Gable, Annika L.
Fuller, Jonathan C.
Bruce, Neil J.
Richter, Stefan
Wade, Rebecca C.
author_sort Yu, Xiaofeng
collection PubMed
description 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/.
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spelling pubmed-44893112015-07-07 webSDA: a web server to simulate macromolecular diffusional association Yu, Xiaofeng Martinez, Michael Gable, Annika L. Fuller, Jonathan C. Bruce, Neil J. Richter, Stefan Wade, Rebecca C. Nucleic Acids Res Web Server issue 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/. Oxford University Press 2015-07-01 2015-04-16 /pmc/articles/PMC4489311/ /pubmed/25883142 http://dx.doi.org/10.1093/nar/gkv335 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server issue
Yu, Xiaofeng
Martinez, Michael
Gable, Annika L.
Fuller, Jonathan C.
Bruce, Neil J.
Richter, Stefan
Wade, Rebecca C.
webSDA: a web server to simulate macromolecular diffusional association
title webSDA: a web server to simulate macromolecular diffusional association
title_full webSDA: a web server to simulate macromolecular diffusional association
title_fullStr webSDA: a web server to simulate macromolecular diffusional association
title_full_unstemmed webSDA: a web server to simulate macromolecular diffusional association
title_short webSDA: a web server to simulate macromolecular diffusional association
title_sort websda: a web server to simulate macromolecular diffusional association
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489311/
https://www.ncbi.nlm.nih.gov/pubmed/25883142
http://dx.doi.org/10.1093/nar/gkv335
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