Thymidine Kinase - The flexibility of the protein and the presence of the water molecules made this specific test case the perfect validation for FITTED. The two structures 1e2k and 1ki3 show different side-chain orientation for residue GLN125 upon binding with the ligand. Moreover, the presence of the two water molecules in 1e2k are displaced by the ligand in 1ki3. FITTED was able to reproduce both binding poses for the respective structures. It was also able to re-assign the correct protein structure and water molecules throughout the docking process. (Corbeil, C. R. et al. J Chem Inf Model, 2007, 47, 435-449)
Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs - We demonstrated the impact of protein and ligand conformations as well as protein flexibility and water molecules on the accuracy of docking programs. These biases were investigated within FITTED2.6 along with FlexX, GOLD, Glide, and Surflex.The input ligand conformation was found to have a major impact on the program accuracy as drops as large as 10-50% were observed with all the programs but FITTED. This comparative study also demonstrates that the accuracy of FITTED is similar to that of other widely used programs. (J. Chem. Inf. Model., 2009, 49 (4), pp 997–1009)
