EML Research is pleased to announce the release of version 5 of SDA at:
http://projects.eml.org/mcm/software/SDA.
SDA can be used to simulate the diffusional association of two proteins or other molecules given the atomic structure of the bound complex of the two molecules. SDA can be used to calculate bimolecular association rates, record Brownian dynamics trajectories or encounter complexes and calculate bimolecular electron transfer rate constants.
New features in SDA5 include the addition of non-polar desolvation forces to the existent electrostatic forces, and options to compute electron transfer rate constants. These are described in a recent application to study protein-protein electron transfer, see:
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 9230-9238. doi:10.1006/jmbi.1999.2919.
A number of new analysis tools have been added and the software has been modified for improved flexibility and efficiency.
SDA is freely available for academic and non-commercial use and can be downloaded from http://projects.eml.org/mcm/software/SDA. Commercial users may acquire a license.
This version of SDA has been developed in the Molecular and Cellular Modeling Group (MCM) at EML Research with the support of the Klaus Tschira Foundation and the Center for Modelling and Simulation in the Biosciences (BIOMS) in Heidelberg.
The authors can be contacted through the MCM software manager at:
mcmsoft@eml-r.villa-bosch.de
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Telephone: +49 (0)6221 - 533 - 279
Fax: +49 (0)6221 - 533 - 298
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