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B. L. Grigorenko, A. V. Nemukhin, I. A. Topol and S. K. Burt, “Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique:? Proposal of Flexible Fragments,” The Journal of Physical Chemistry A, Vol. 106, No. 44, 2002, pp. 10663-10672. doi:10.1021/jp026464w

has been cited by the following article:

• TITLE: Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

  AUTHORS: I. Topol, J. Collins, A. Nemukhin

  KEYWORDS: Chromophore-Containing Pockets; Coordinate-Locking Scheme; ZINDO; Photoswitchable Fluorescent Proteins; Asfp595

  JOURNAL NAME: Computational Molecular Bioscience, Vol.2 No.3, September 20, 2012

  ABSTRACT: An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.