A computer-based modeling and bench-top experiments are combined to understand the fluorescence of GFP. Random octapeptides are inserted into individual loops of the GFP. Amino acid sequences and fluorescence levels of clones from each loop are determined. The effect of peptide insertions into the loop regions of GFP are studied computationally using quantum mechanics and molecular dynamics calculations. Our experimental and computational results show that the random peptide insertions into the loop regions change the absorption intensity of the GFP but not the absorption wavelength. (c) 2005 Elsevier B.V. All rights reserved.