In the current work a method for the elucidation of the spatial structure of fluorescent GFP-like proteins is presented. The method is based on combining the results of homology modeling of the overall spatial protein structure and the chromophore structure determined experimentally by mass spectrometry. The approach developed can be used for the determination of the spatial structure of GFP homologues which are difficult to crystallize. © 2011 Pleiades Publishing, Ltd.