Hi, Gaiser, may be this paper will be usefull.

http://books.google.de/books?id=-PSybuLNxcAC&pg=PA912&lpg=PA912&dq=protein+fluorescence+property/intensity+prediction&source=bl&ots=xdtZkGvlRT&sig=Zdaw1qFYyJ5pTqTWfgHEYkEZV8w&hl=de&sa=X&ei=-s5oVLXNDYG6PYbbgaAE&ved=0CEQQ6AEwBA#v=onepage&q=protein%20fluorescence%20property%2Fintensity%20prediction&f=false

Do you want to predict also fluoresence of the GFP in cells? It may also dependent form a couple of factors and can be far from theretically predicted.

I have seen people using DFT to calculate some absorption spectra, CD and raman, ground state -> excited state... but not fluorescence properties.

http://www.opticsinfobase.org/as/abstract.cfm?uri=as-63-7-733

http://www.sciencedirect.com/science/article/pii/S0010854508001197

Since fluorescence emission usually probes the excited state processes, that can happen on nanosecond scales, some people have use regular MD to explain quenching due to waters on GFPs.... however, i guess QM could be applied if the system is greatly simplified.

http://pubs.acs.org/doi/abs/10.1021/jp308366y

i hope this helps.

Hi,

There are two factors that can influence the fluorescent properties of Green Fluorescent Protein, which are the extent of the chemical conjugation of chromophores and the surrounding protein environments of the chromophores. For example, Blue Fluorescent Protein was made from changing the structure of the chromophore in which Tyrosine is mutated to Histidine. Yellow Fluorescent Protein was made from changing the environmental residue of the chromophore where Tyrosine 203 create a pi-pi stacking interaction chromophore, which in turns give rise to the red-shifted in the fluorescent properties. Recently, we have utilized the Proteochemometrics modeling to elucidate the spectral properties of GFP by considering descriptors from both  structure variants of the chromophore as well as the surrounding amino acids of the chromphore. Please see the attached file.  Thank you.

Article Illuminating the Origins of Spectral Properties of Green Flu...

Hi Qaiser, semi-empirical methods or quantum mechanical methods are suitable for isolated chromophores but if you would like to study the fluorescent properties of the chromophore within the context of the full-length GFP, I would recommend QM/MM whereby the chromophore is treated at the QM level while the surrounding protein at the MM level. Studying the chromophore alone may miss out on potential effects from surrounding residues as Saw had pointed out above as well as discussed in detail in the last link provided below. See the first 3 links below for further information on QM/MM as applied to GFP.

http://pubs.acs.org/doi/abs/10.1021/ct200704k

http://pubs.acs.org/doi/abs/10.1021/jp208749v

http://dx.doi.org/10.1002/bip.20156

http://dx.doi.org/10.1562/2005-04-11-RA-485