Nucleic Acids Research . Vol. 40, W380-W386 . doi: 10.1093/nar/gks401. HTML PDF 2. Spriggs RV, Artymiuk PJ, Willett P. (2003) Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci . Mar-Apr;43(2):412-21. The IMAAAGINE program allows users to search for hypothetical amino acid 3D arrangement query to be searched against the PDB.
Users design their own motif with specific residue types and distances between residues, with a flexible distance tolerance. Go to IMAAAGINE main page Input / Query file: Distanced based theoretical arrangement of amino acid residues (menu based selection and wild-card capability) Database searched: PDB and PDB subsets Primary Reference.