• fluorescent proteins;
  • photoreceptor proteins;
  • structure;
  • optical spectra;
  • density functional theory;
  • ZINDO;
  • SOS-CIS(D)

This Perspective describes some of the recent successes in modeling properties of chromophore containing domains of proteins capable to respond to visible light by using quantum chemistry methods. Applications to two distinctively different classes of such proteins are considered: those of the green fluorescent protein family with the chromophores derived from the hydroxybenzylidene-imidazolinone moiety and those containing the flavin-based chromophore. The major emphasis is on applications of economic computational strategies to estimate geometry configurations and electronic excitation energies. We show that using the molecular cluster approach and the “black-box” methods ZINDO and SOS-CIS(D) proves to be efficient for characterization of protein spectra. © 2013 Wiley Periodicals, Inc.