webSDACitation

Citation

Cite webSDA:

webSDA: a web server to simulate macromolecular diffusional association
Xiaofeng Yu; Michael Martinez; Annika L. Gable; Jonathan C. Fuller; Neil J. Bruce; Stefan Richter; Rebecca C. Wade
Nucleic Acids Research 2015; 43 (W1): W220-W224 (Article doi: 10.1093/nar/gkv335v1)

Cite SDA

webSDA uses a variety of in-house and third party tools. Depending on your calculations, you will need to decide which cite.
The following three should always be cited:


Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC. SDA7: A Modular and Parallel Implementation of the Simulation of Diffusional Association Software.  J. Comput. Chem. (2015) 36, 1631-1645. (Article, Google Scholar Citations)
Gabdoulline RR and Wade RC.  Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter.  Methods (1998) 3 , 329-341. (Article, Google Scholar Citations)
Gabdoulline RR and Wade RC.  Simulation of the Diffusional Association of Barnase and Barstar.  Biophys. J. (1997) 72 , 1917-1929. (Article, Google Scholar Citations)

PDB files used

Dolinsky TJ, Nielsen JE, McCammon JA and Baker NA.  PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.  Nucleic Acids Res. (2004) 32 , W665-W667. (Article)

Electrostatic interaction used

Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA.  Electrostatics of nanosystems: application to microtubules and the ribosome.  Proc. Natl. Acad. Sci. USA (2001) 98 , 10037-10041. (Article)

Gabdoulline RR and Wade RC.  Effective Charges for Macromolecules in Solvent.  J. Phys. Chem. (1996) 100 , 3868–3878. (Article)

Electrostatic desolvation used

Elcock AH, Gabdoulline RR, Wade RC and McCammon JA.  Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin.  J. Mol. Biol. (1999) 291 , 149-162. (Article)

Non-polar desolvation used

Gabdoulline RR and Wade RC.  On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f : Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events.  J. Am. Chem. Soc. (2009) 131 , 9320-9238. (Article)

Methods

SDA docking

Motiejunas D, Gabdoulline RR, Wang T, Feldman-Salit A, Johann T, Winn PJ and Wade RC.  Protein–protein docking by simulating the process of association subject to biochemical constraints.  Proteins. (2008) 71 , 1955–1969. (Article)

SDA multiple molecules

Mereghetti P, Gabdoulline R, and Wade RC.  Brownian dynamics simulation of protein solutions: Structural and dynamical properties.  Biophys. J. (2010) 99 , 3782-3791. (Article)

Usage examples

You can find these here: SDA 7 website