title: webSDA: a web server to simulate macromolecular diffusional association.
abstract: 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/.
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany Rebecca.Wade@h-its.org.
authors.forename: Xiaofeng
authors.identifier: http://orcid.org/0000-0001-6742-3591
authors.initials: X
authors.lastname: Yu
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Martinez
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany.
authors.forename: Annika L
authors.initials: AL
authors.lastname: Gable
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany.
authors.forename: Jonathan C
authors.initials: JC
authors.lastname: Fuller
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany.
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Bruce
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Richter
authors.affiliation: Molecular and Cellular Modeling group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Baden-Württemberg, Germany Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Baden-Württemberg, Germany Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Baden-Württemberg, Germany Rebecca.Wade@h-its.org.
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Wade
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D020407:Internet; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA