SARA is a very fast method for doing single side chain replacements in protein structures by using a coarse- grained method. It is over five times faster than the leading all-atom approach, and generates biologically realistic side-chain angles. The solutions found by SARA typically deviate less than 1 ? and 12 degrees from native structures or the best all-atom solution. Run-time for the algorithm is highly predictable and can easily be tuned by the user. These characteristics makes SARA an excellent choice for high-throughput applications like structural genomics, evolutionary simulations and structure-based phylogenetics.
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J Mol Evol. 2011 Aug;73(1-2):23-33. Epub 2011 Jul 29.
Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.
Grahnen JA, Kubelka J, Liberles DA.