FAST Alignment and Search Tool

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FAST Alignment and Search Tool (or, just FAST) is a new algorithm for aligning three-dimensional structures of proteins.[1] FAST employs an elimination heuristic to quickly and reliably detect the global optimum residue-residue alignment. The main application is detection of structural and functional similarities that are not available with traditional sequence alignment algorithms. FAST can be run from the web by uploading two PDB files in the given form. Or, one can also download the executable for off-line use.

FAST is developed by Jianhua Zhu at the Bioinformatics Program of Boston University.


% fast protein1 protein2 [-r rasmol-script]

%1              fn      protein #1
%2              fn      protein #2
-o|--out        fn      output file name [stdout]
-r|--rasmol     fn      generate a rasmol script for the alignment
-p|--path       fn      path to protein structures
-h|--help               display this message

To visualize alignment under Linux:

% rasmol -script rasmol-script


  1. Zhu J, Weng Z (2005). FAST: a novel protein structure alignment algorithm. Proteins: Structure, Function and Bioinformatics (14):417-423.

See also

External links